Contacts of the helix formed by residues 634 - 652 (chain C) in PDB entry 4MNE
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 SER 634 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ILE* 3.9 17.8 - - - +
601C LYS* 4.2 9.9 - - - +
633C TYR* 1.3 78.7 - - - +
635C PHE* 1.3 66.0 + - - +
636C GLN* 2.8 30.1 + - - +
637C SER* 2.8 30.1 + - - -
638C ASP 3.5 1.6 + - - -
701C ARG* 3.8 25.2 - - - -
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Residues in contact with PHE 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568C HIS* 3.3 68.7 - + + +
571C SER* 4.0 16.8 - - - -
572C ILE 4.0 7.4 - - - -
573C ILE* 4.1 16.4 - - + +
601C LYS* 4.5 19.9 - - + +
634C SER* 1.3 73.5 - - - +
636C GLN* 1.3 71.2 + - - +
638C ASP* 3.2 9.7 + - - +
639C VAL* 3.2 22.5 + - - +
706C LEU* 4.0 20.6 - - + -
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Residues in contact with GLN 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634C SER* 2.8 18.5 + - - +
635C PHE* 1.3 87.9 + - - +
637C SER* 1.3 55.6 + - - +
639C VAL* 3.1 12.3 + - - +
640C TYR 3.0 23.0 + - - -
701C ARG* 3.6 35.0 - - + +
702C ASP* 4.6 15.5 + - - +
704C ARG* 3.0 26.0 + - + +
706C LEU* 3.6 33.2 - - + +
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Residues in contact with SER 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C ILE* 4.6 1.4 - - - +
575C ARG* 5.6 0.2 - - - -
619C TRP 4.9 1.2 - - - +
621C ALA* 4.4 4.2 + - - +
623C GLU* 4.2 6.1 - - - -
624C VAL* 3.8 27.4 - - - -
632C PRO 4.5 0.9 - - - -
633C TYR* 3.7 14.2 - - - +
634C SER* 2.8 34.1 + - - -
636C GLN* 1.3 77.0 - - - +
638C ASP* 1.3 64.7 + - - +
640C TYR* 3.1 6.1 + - - +
641C ALA* 3.1 21.0 + - - +
704C ARG* 3.8 9.1 - - - +
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Residues in contact with ASP 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C MET* 3.6 16.3 - - + +
568C HIS* 3.1 25.7 + - + +
573C ILE* 3.6 10.7 - - - +
574C HIS* 2.8 28.5 + - - +
575C ARG* 3.1 25.7 + - - -
576C ASP 4.6 0.9 + - - -
577C LEU* 3.8 10.5 + - - +
634C SER 3.5 0.6 + - - -
635C PHE 3.2 11.1 + - - +
637C SER* 1.3 82.4 + - - +
639C VAL* 1.3 57.2 + - - +
641C ALA* 3.3 8.0 - - - +
642C PHE* 2.8 26.7 + - - +
707C PHE* 4.5 2.2 - - - -
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Residues in contact with VAL 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635C PHE 3.4 14.8 - - - +
636C GLN* 3.1 14.1 + - - +
638C ASP* 1.3 74.6 - - - +
640C TYR* 1.3 60.5 + - - +
642C PHE* 3.2 9.2 + - - +
643C GLY* 2.8 26.2 + - - -
696C CYS* 3.9 23.8 - - + +
704C ARG* 4.4 6.1 - - + -
705C PRO* 3.4 27.6 - - + +
706C LEU* 4.6 5.6 - - + -
707C PHE* 3.8 22.7 - - + -
710C ILE* 3.7 17.9 - - + -
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Residues in contact with TYR 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C LEU 4.8 2.0 + - - -
619C TRP 3.5 8.3 - - - -
620C MET 3.1 23.1 + - - -
621C ALA* 3.3 30.5 - - + -
622C PRO* 4.1 12.6 - - + +
636C GLN 3.0 6.3 + - - -
637C SER 3.1 9.4 + - - +
639C VAL* 1.3 72.7 - - - +
641C ALA* 1.3 65.4 + - - +
643C GLY* 2.8 13.0 + - - -
644C ILE* 2.9 36.5 + - + +
656C TYR* 3.5 20.4 + - - -
669C VAL* 4.5 7.4 - - - +
676C PRO* 4.4 5.7 - - + +
696C CYS 3.5 8.2 + - - -
697C LEU* 3.5 43.7 - - + +
704C ARG* 3.8 18.2 - - - +
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Residues in contact with ALA 641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577C LEU* 3.4 33.2 - - + +
619C TRP* 3.5 22.4 - - + +
637C SER 3.1 11.4 + - - +
638C ASP* 3.3 13.9 - - - +
640C TYR* 1.3 74.8 - - - +
642C PHE* 1.3 64.9 + - - +
644C ILE* 3.0 8.0 + - - +
645C VAL* 2.9 25.2 + - - +
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Residues in contact with PHE 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557C ALA* 3.7 25.4 - - - -
560C THR* 3.8 27.1 - - + -
561C ALA* 4.0 13.5 - - + -
577C LEU* 3.8 10.4 - - + +
638C ASP 2.8 17.0 + - - +
639C VAL 3.2 7.9 - - - +
641C ALA* 1.3 72.6 - - - +
643C GLY* 1.3 50.1 + - - +
645C VAL* 2.9 14.3 + - + +
646C LEU* 2.7 64.3 + - + +
649C LEU* 6.2 0.2 - - + -
696C CYS* 4.3 6.3 - - - -
707C PHE* 3.6 26.0 - + + -
710C ILE* 3.6 30.1 - - + -
714C ILE* 4.2 5.8 - - + -
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Residues in contact with GLY 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639C VAL 2.8 17.2 + - - -
640C TYR 2.8 8.0 + - - -
642C PHE* 1.3 67.6 - - - +
644C ILE* 1.3 57.7 + - - -
646C LEU* 3.1 11.1 + - - +
647C TYR* 2.7 27.9 + - - +
693C MET* 4.1 5.6 - - - +
696C CYS* 3.8 19.7 - - - -
697C LEU* 3.7 13.9 - - - +
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Residues in contact with ILE 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C LEU 3.5 24.7 - - - +
619C TRP* 3.4 30.3 - - + +
640C TYR* 2.9 35.4 + - + +
641C ALA 3.4 7.6 - - - +
643C GLY* 1.3 75.8 - - - +
645C VAL* 1.3 64.0 + - - +
647C TYR* 3.0 9.5 + - + +
648C GLU* 2.9 26.4 + - - +
655C PRO* 4.0 23.6 - - + -
656C TYR* 4.7 1.3 - - - +
676C PRO* 3.9 17.0 - - + -
697C LEU* 3.6 18.2 - - + -
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Residues in contact with VAL 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C LEU* 4.2 17.7 - - + -
560C THR* 5.2 5.6 - - + +
577C LEU* 4.6 5.4 - - + -
578C LYS* 4.3 4.5 - - - -
579C SER* 4.1 14.6 - - - +
582C ILE* 3.9 27.8 - - + -
619C TRP* 4.1 15.3 - - + +
641C ALA 2.9 19.3 + - - +
642C PHE* 2.9 17.3 + - + +
644C ILE* 1.3 74.1 - - - +
646C LEU* 1.3 64.4 + - - +
648C GLU* 3.1 13.5 + - - +
649C LEU* 2.9 29.9 + - + +
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Residues in contact with LEU 646 (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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557C ALA* 3.7 29.6 - - + -
642C PHE* 2.7 44.2 + - + +
643C GLY* 3.2 10.3 - - - +
645C VAL* 1.3 72.6 - - - +
647C TYR* 1.3 57.2 + - - +
649C LEU* 3.1 11.6 + - + +
650C MET* 2.8 35.7 + - + +
689C MET* 4.2 19.5 - - - -
692C LEU* 4.1 15.7 - - + +
693C MET* 4.0 36.3 - - + +
696C CYS* 4.7 2.9 - - - -
714C ILE* 5.3 0.2 - - + -
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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
----------------------------------------------------------
643C GLY 2.7 16.1 + - - +
644C ILE* 3.0 17.5 - - + +
646C LEU* 1.3 72.4 - - - +
648C GLU* 1.3 62.9 + - - +
650C MET 3.1 1.6 + - - -
651C THR* 2.9 55.6 + - + +
653C GLN* 3.8 7.7 + - + +
654C LEU 3.7 7.7 + - - -
655C PRO* 3.7 36.5 - - + +
656C TYR 5.2 0.9 + - - -
676C PRO* 3.8 26.9 - - + -
677C ASP* 3.0 37.0 + - - +
678C LEU* 4.6 5.4 - - + -
680C LYS* 3.8 13.0 - - - +
693C MET* 3.9 23.2 - - + -
697C LEU* 5.0 4.7 - - + -
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Residues in contact with GLU 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LEU* 3.7 15.7 - - + +
542C HIS* 2.5 31.8 + - - +
579C SER* 2.6 30.2 + - - -
619C TRP* 2.8 37.6 + - - -
644C ILE* 2.9 20.0 + - + +
645C VAL* 3.5 9.5 - - - +
647C TYR* 1.3 73.0 - - + +
649C LEU* 1.3 57.0 + - - +
652C GLY* 2.6 34.0 + - - -
653C GLN 3.3 20.9 - - - +
654C LEU* 3.7 4.9 - - + +
655C PRO* 5.0 2.0 - - + -
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Residues in contact with LEU 649 (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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537C LEU* 3.7 30.7 - - + -
541C LEU* 4.3 7.5 - - + +
553C LEU* 3.6 34.2 - - + +
556C ILE* 4.2 16.4 - - + -
557C ALA* 4.0 34.8 - - + +
560C THR* 5.7 0.4 - - - +
642C PHE* 6.2 0.2 - - + -
645C VAL* 2.9 28.4 + - + +
646C LEU* 3.4 14.1 - - + +
648C GLU* 1.3 77.2 - - - +
650C MET* 1.3 62.4 - - + +
682C ARG* 2.5 32.1 + - - -
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Residues in contact with MET 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C MET* 3.9 31.4 - - - +
553C LEU* 4.2 21.1 - - + +
554C ILE* 4.4 2.7 - - + -
557C ALA* 5.2 0.2 - - + -
646C LEU* 2.8 25.9 + - + +
647C TYR 4.2 0.9 - - - +
649C LEU* 1.3 82.7 - - + +
651C THR* 1.3 59.6 + - - +
681C VAL* 3.3 5.4 - - + -
682C ARG* 2.8 34.8 + - - +
685C CYS* 3.8 20.3 - - - +
689C MET* 3.6 37.9 - - + -
693C MET* 3.8 26.2 - - + -
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Residues in contact with THR 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647C TYR* 2.9 44.8 + - + +
650C MET* 1.3 78.6 - - + +
652C GLY* 1.3 63.3 + - - +
653C GLN* 2.7 40.3 + - - +
680C LYS* 3.7 22.1 - - + +
681C VAL* 3.6 25.8 - - + +
682C ARG* 4.2 13.2 + - - +
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Residues in contact with GLY 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C LEU* 4.0 15.1 - - - +
542C HIS* 3.7 16.5 + - - -
545C GLU* 6.0 0.3 - - - +
648C GLU 2.6 24.2 + - - -
650C MET 3.8 0.4 - - - -
651C THR* 1.3 73.6 - - - +
653C GLN* 1.3 60.0 + - - +
682C ARG* 3.7 21.0 - - - +
104D LYS* 5.7 2.3 + - - -
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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