Contacts of the helix formed by residues 635 - 657 (chain C) in PDB entry 4PE5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 635 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634C MET* 1.3 75.6 - - - +
636C TRP* 1.3 61.2 + - - +
638C GLY* 3.1 3.4 + - - +
639C PHE* 2.9 28.8 + - - +
824D MET 5.3 1.8 - - - +
828D ALA* 3.8 29.4 - - + -
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Residues in contact with TRP 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C VAL* 5.3 13.2 - - + -
613C VAL* 5.5 7.7 - - + +
634C MET 3.4 4.3 - - - +
635C VAL* 1.3 78.4 - - - +
637C ALA* 1.3 59.2 + - - +
639C PHE* 3.4 6.3 + - - +
640C ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C VAL* 5.2 11.8 - - + +
634C MET* 3.6 16.4 + - - +
635C VAL 3.2 0.4 - - - -
636C TRP* 1.3 75.7 - - - +
638C GLY* 1.3 59.8 + - - +
640C ALA* 3.6 6.8 - - - +
641C MET* 2.9 30.0 + - - +
611D GLY* 6.2 4.5 - - - -
614D PHE* 4.4 14.1 - - + +
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Residues in contact with GLY 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634C MET 3.3 9.4 + - - -
635C VAL* 3.1 7.6 + - - -
637C ALA* 1.3 79.0 - - - +
639C PHE* 1.3 56.9 + - - +
641C MET* 3.4 5.0 + - - +
642C ILE* 2.9 29.5 + - - +
614D PHE* 5.9 0.4 - - - -
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Residues in contact with PHE 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635C VAL 2.9 15.0 + - - +
636C TRP* 3.9 7.6 - - - +
638C GLY* 1.3 74.2 - - - +
640C ALA* 1.3 58.8 + - - +
642C ILE* 3.8 7.0 - - - +
643C ILE* 2.9 29.6 + - - +
821D VAL* 5.7 12.1 - - + +
824D MET* 5.8 9.0 - - + -
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Residues in contact with ALA 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613C VAL* 3.8 24.5 - - + +
614C LEU* 4.3 15.3 - - + +
636C TRP 2.9 18.2 + - - +
637C ALA* 3.6 8.3 - - - +
638C GLY 3.2 0.2 - - - -
639C PHE* 1.3 74.7 - - - +
641C MET* 1.3 59.3 + - - +
643C ILE* 3.3 5.5 + - - +
644C VAL* 2.9 29.9 + - - +
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Residues in contact with MET 641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637C ALA 2.9 18.4 + - - +
638C GLY* 3.8 5.8 - - - +
640C ALA* 1.3 76.2 - - - +
642C ILE* 1.3 58.0 + - - +
644C VAL* 3.5 5.7 + - - +
645C ALA* 2.9 31.0 + - - +
614D PHE* 4.0 22.4 - - + -
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Residues in contact with ILE 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638C GLY 2.9 19.0 + - - +
639C PHE* 3.8 7.9 - - - +
641C MET* 1.3 76.4 - - - +
643C ILE* 1.3 59.7 + - - +
645C ALA* 3.8 4.2 - - - +
646C SER* 2.9 30.8 + - - -
550D PHE* 6.2 4.5 - - + -
821D VAL* 6.5 0.7 - - + -
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Residues in contact with ILE 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566C VAL* 6.2 4.3 - - + -
639C PHE 2.9 20.1 + - - +
640C ALA* 3.7 6.5 - - - +
642C ILE* 1.3 73.8 - - - +
644C VAL* 1.3 60.8 + - - +
646C SER* 3.8 5.6 - - - -
647C TYR* 2.9 29.3 + - - +
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Residues in contact with VAL 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ALA* 5.6 0.9 - - - +
614C LEU 6.1 0.9 - - - +
640C ALA 2.9 17.5 + - - +
641C MET* 3.8 6.5 - - - +
643C ILE* 1.3 75.4 - - - +
645C ALA* 1.3 59.9 + - - +
647C TYR* 3.2 8.1 + - - +
648C THR* 2.9 29.7 + - - -
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Residues in contact with ALA 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641C MET 2.9 18.6 + - - +
642C ILE* 3.9 5.6 - - - +
644C VAL* 1.3 76.9 - - - +
646C SER* 1.3 57.5 + - - +
648C THR* 3.4 6.0 + - - -
649C ALA* 2.9 30.5 + - - +
646D TYR* 4.2 23.1 - - + +
647D THR* 4.9 10.5 - - - -
650D LEU* 4.6 5.9 - - + +
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Residues in contact with SER 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642C ILE 2.9 19.7 + - - -
643C ILE* 3.8 6.3 - - - -
645C ALA* 1.3 73.8 - - - +
647C TYR* 1.3 61.0 + - - +
649C ALA* 3.9 5.4 - - - +
650C ASN* 2.9 31.9 + - - +
650D LEU* 5.9 0.7 - - - -
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Residues in contact with TYR 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ILE* 4.2 25.0 + - + +
644B ALA* 3.6 29.6 - - + -
645B SER 5.4 0.2 - - - -
554C PHE* 5.2 9.9 + - - -
555C MET 5.2 2.3 + - - -
556C GLN* 5.0 4.7 - - + -
557C PRO* 3.6 34.8 - - + +
558C PHE* 5.5 8.7 - - + -
643C ILE 2.9 19.5 + - - +
644C VAL* 3.5 7.9 - - - +
646C SER* 1.3 77.9 - - - +
648C THR* 1.3 55.6 + - - +
650C ASN* 4.0 3.8 - - - +
651C LEU* 2.9 38.2 + - + +
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Residues in contact with THR 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ALA* 4.4 24.0 - - - +
647B THR* 5.7 7.9 - - - -
648B ALA* 4.2 4.0 - - - +
644C VAL 2.9 17.6 + - - -
645C ALA* 3.8 7.2 - - - -
647C TYR* 1.3 79.1 - - - +
649C ALA* 1.3 56.7 + - - +
651C LEU* 3.4 6.1 + - - +
652C ALA* 2.9 29.6 + - - +
647D THR* 5.3 10.8 - - - -
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Residues in contact with ALA 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645C ALA 2.9 18.4 + - - +
646C SER* 3.9 5.6 - - - +
648C THR* 1.3 79.3 - - - +
650C ASN* 1.3 56.4 + - - +
652C ALA* 3.3 5.4 + - - +
653C ALA* 2.9 28.6 + - - +
647D THR 4.6 2.9 + - - +
650D LEU* 3.7 37.5 - - + +
651D ALA* 3.9 11.1 - - + +
654D MET* 4.3 8.1 - - + +
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Residues in contact with ASN 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C PRO* 4.7 18.7 - - + +
646C SER 2.9 19.1 + - - +
647C TYR* 4.0 4.9 - - - +
649C ALA* 1.3 73.4 - - - +
651C LEU* 1.3 59.1 + - - +
653C ALA* 3.8 6.6 - - - +
654C PHE* 2.9 32.1 + - - +
654D MET* 5.2 3.1 - - - +
809D MET 5.0 1.9 - - - +
810D SER* 6.1 0.9 - - - -
811D SER* 5.1 18.2 - - - +
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Residues in contact with LEU 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ALA* 5.4 3.8 - - + +
645B SER* 5.5 2.5 - - - +
648B ALA* 3.7 16.4 - - + +
557C PRO* 5.0 8.0 - - + +
647C TYR* 2.9 33.4 + - + +
648C THR* 3.7 6.3 - - - +
649C ALA 3.3 0.4 - - - -
650C ASN* 1.3 76.7 - - - +
652C ALA* 1.3 59.9 + - - +
654C PHE* 3.8 7.7 + - - +
655C LEU* 3.4 19.4 - - - +
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Residues in contact with ALA 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B ALA* 3.7 25.6 - - + +
651B ALA* 5.0 9.0 - - + -
648C THR 2.9 17.5 + - - +
649C ALA* 3.5 7.9 - - - +
651C LEU* 1.3 77.3 - - - +
653C ALA* 1.3 60.0 + - - +
655C LEU* 3.4 1.0 + - - +
656C VAL* 2.9 36.0 + - + +
651D ALA* 4.4 15.5 - - + -
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Residues in contact with ALA 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C ALA 2.9 17.5 + - - +
650C ASN* 3.4 6.0 + - - +
652C ALA* 1.3 75.9 - - - +
654C PHE* 1.3 57.7 + - - +
655C LEU 3.1 5.5 + - - -
656C VAL* 5.1 1.6 - - - -
657C LEU* 3.8 23.5 + - - +
651D ALA 5.4 0.9 + - - +
654D MET* 3.3 31.6 - - + +
655D ILE* 4.6 11.7 - - + -
808D VAL* 4.2 7.8 - - - +
809D MET 5.3 3.6 - - - +
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Residues in contact with PHE 654 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C PRO* 5.5 8.5 - - + -
650C ASN 2.9 18.8 + - - +
651C LEU* 3.9 6.4 - - - +
652C ALA 3.3 0.6 - - - -
653C ALA* 1.3 75.0 - - - +
655C LEU* 1.3 60.2 + - - +
657C LEU 6.0 0.4 - - - -
808D VAL* 5.4 5.2 - - - -
809D MET* 3.9 20.0 - - - +
810D SER* 5.7 1.1 - - - -
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Residues in contact with LEU 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B ALA* 5.3 5.2 - - + +
649B ASN* 5.5 2.7 - - - +
652B ALA* 4.3 13.0 - - + -
651C LEU 3.4 16.8 - - - +
652C ALA* 3.9 3.4 - - - +
653C ALA 3.1 2.0 + - - -
654C PHE* 1.3 81.2 - - - +
656C VAL* 1.3 65.8 + - - +
657C LEU* 3.3 10.6 + - - +
805C PRO* 3.9 19.2 - - + +
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Residues in contact with VAL 656 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B ALA* 5.4 3.8 - - + -
652B ALA* 4.2 21.7 - - + +
655B ILE* 4.9 14.6 - - + +
652C ALA* 2.9 18.4 + - + +
653C ALA* 5.1 2.5 - - - -
655C LEU* 1.3 77.7 - - - +
657C LEU* 1.3 60.7 + - - +
805C PRO* 4.8 9.7 - - - +
655D ILE* 6.0 5.4 - - + -
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Residues in contact with LEU 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C ALA* 3.8 12.4 + - - +
654C PHE 6.0 0.2 - - - -
655C LEU* 3.3 12.9 - - - +
656C VAL* 1.3 84.5 - - - +
658C ASP* 1.3 66.6 + - - +
805C PRO* 5.9 1.0 - - - +
655D ILE* 6.2 3.8 - - + -
807D GLU 5.9 0.4 - - - -
808D VAL* 3.6 23.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il