Contacts of the helix formed by residues 628 - 642 (chain C) in PDB entry 5MKE
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 THR 628 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B SER* 5.0 11.4 - - - +
245B ASN* 6.2 0.2 - - - -
247B TYR* 3.9 6.1 - - + -
248B TYR* 3.4 36.3 - - + +
382C ILE* 4.5 17.4 - - + +
383C ILE* 5.5 5.2 - - + -
616C TYR* 4.8 0.2 - - - -
626C PHE 3.1 2.6 + - - -
627C SER* 1.3 78.9 - - - +
629C PHE* 1.3 53.4 + - - +
630C GLN* 3.1 9.8 - - - +
631C GLU* 2.5 61.0 + - - +
632C CYS 3.5 0.9 + - - -
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Residues in contact with PHE 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B SER* 5.1 4.0 - - - -
1005B CHS 4.5 52.0 - - + +
609C LEU* 3.5 34.3 - - + -
612C ALA* 4.0 6.7 - - + -
613C GLN* 3.7 36.1 - - + -
616C TYR* 3.8 40.2 - + + -
627C SER 3.7 2.0 - - - -
628C THR* 1.3 69.9 - - - +
630C GLN* 1.3 68.2 + - - +
632C CYS* 3.1 15.7 + - + +
633C ILE* 3.4 8.6 + - + -
1010C PLM 4.5 16.8 - - + +
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Residues in contact with GLN 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C TRP* 5.1 8.5 - - - -
382C ILE* 4.0 29.9 + - - +
628C THR* 2.7 13.3 + - - +
629C PHE* 1.3 79.3 - - - +
631C GLU* 1.3 62.6 + - + +
633C ILE* 2.5 43.0 + - + +
634C PHE* 3.5 11.1 + - + -
1009C PLM 2.9 38.5 + - + +
1010C PLM 4.7 20.0 - - + +
650D GLU* 5.9 0.8 + - - -
654D ARG* 5.7 3.8 + - - +
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Residues in contact with GLU 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TYR* 5.6 2.6 - - - -
248B TYR* 5.3 2.8 + - - -
382C ILE* 5.1 5.9 - - - +
625C ASP* 3.5 39.4 + - - +
626C PHE 4.5 1.9 + - - +
628C THR* 2.5 36.3 + - - +
630C GLN* 1.3 78.0 - - + +
632C CYS* 1.3 55.0 + - - +
634C PHE* 2.9 31.9 + - + +
635C THR* 2.9 15.8 + - - +
650D GLU* 6.2 6.1 - - + -
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Residues in contact with CYS 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612C ALA* 3.8 23.2 - - + +
616C TYR* 4.5 10.8 - - - -
625C ASP 4.0 4.9 - - - -
626C PHE* 3.2 26.5 - - + -
627C SER* 2.6 42.4 - - - -
628C THR 3.5 0.2 + - - -
629C PHE* 3.1 14.5 + - + +
630C GLN 3.1 0.8 - - - -
631C GLU* 1.3 76.6 - - - +
633C ILE* 1.3 61.9 + - - +
635C THR* 4.0 4.4 - - - +
636C GLN* 3.3 22.5 + - - +
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Residues in contact with ILE 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C PHE* 3.3 41.5 - - + -
609C LEU* 3.5 32.1 - - + -
612C ALA* 4.1 3.1 - - + +
629C PHE* 3.4 7.1 + - + +
630C GLN* 2.5 31.9 + - + +
632C CYS* 1.3 74.8 - - - +
634C PHE* 1.3 75.4 + - + +
636C GLN* 3.4 8.7 - - - +
637C PHE* 2.9 30.5 + - + -
1009C PLM 4.9 15.7 - - + -
1010C PLM 6.2 3.1 - - + -
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Residues in contact with PHE 634 (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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630C GLN* 3.7 25.6 - - + -
631C GLU* 2.9 18.6 + - + +
633C ILE* 1.3 85.6 - - + +
635C THR* 1.3 50.7 + - - +
636C GLN 2.8 3.8 - - - -
637C PHE* 2.4 33.2 + + - +
638C ARG* 2.7 16.6 + - - -
1009C PLM 5.0 24.9 - - + -
646D PHE* 4.7 17.0 - + + -
650D GLU* 5.5 8.5 - - + -
654D ARG 5.6 1.8 - - - -
658D PRO* 3.8 33.2 - - + -
659D ILE* 4.6 1.8 - - - -
661D PHE* 4.4 16.8 - + + -
662D THR* 3.2 27.6 - - - -
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Residues in contact with THR 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C ASP* 2.5 52.4 + - + +
626C PHE* 3.6 27.4 - - + -
631C GLU* 2.9 10.0 + - - +
632C CYS* 4.4 4.3 - - - -
634C PHE* 1.3 74.7 - - - +
636C GLN* 1.3 58.0 + - - +
638C ARG* 3.7 21.3 + - + +
639C ILE* 3.4 31.7 + - + +
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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
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607C ILE 3.8 0.4 + - - -
608C PHE* 2.2 86.0 + - + +
611C TYR* 3.6 12.1 - - - +
612C ALA* 3.1 25.4 - - - +
626C PHE* 5.6 1.5 - - + -
632C CYS 3.3 14.4 + - - +
633C ILE* 3.4 2.3 - - - +
634C PHE 2.8 1.0 - - - -
635C THR* 1.3 76.8 - - - +
637C PHE* 1.3 59.5 + - - +
639C ILE* 4.5 2.9 - - - -
640C ILE* 3.9 4.5 + - - +
660C TYR* 5.1 7.4 - - - +
664C PHE* 3.7 30.8 - - + -
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Residues in contact with PHE 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604C PHE* 4.9 10.1 - + - -
605C PHE* 6.4 1.1 - + - -
608C PHE* 3.4 25.8 - + - -
633C ILE* 2.9 37.0 - - + -
634C PHE* 2.4 28.6 + + - +
636C GLN* 1.3 66.4 - - - +
638C ARG* 1.3 65.9 + - - +
639C ILE 3.0 2.7 - - - -
640C ILE* 2.9 28.0 - - + +
641C LEU* 3.1 9.0 + - - +
1009C PLM 5.7 2.7 - - + -
661D PHE* 4.6 14.4 - + + -
662D THR* 3.9 35.2 - - + -
665D VAL* 4.4 23.0 - - + +
666D PHE* 5.1 17.5 - + + -
670D PHE* 5.6 7.4 - + - -
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Residues in contact with ARG 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C ASP* 3.4 34.6 + - - +
634C PHE* 2.7 17.7 + - + +
635C THR* 3.7 22.5 + - - +
637C PHE* 1.3 72.8 - - - +
639C ILE* 1.3 49.9 + - + +
641C LEU* 3.5 8.6 + - + +
642C GLY 2.5 39.0 + - - +
643C ASP* 2.6 48.9 + - - +
644C ILE* 5.1 3.3 - - + +
645C ASN* 4.7 11.5 + - - +
644D ILE* 5.4 4.6 + - + -
646D PHE* 5.0 29.6 - - + +
647D ALA* 5.7 4.8 - - - +
661D PHE* 5.0 11.8 - - + -
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Residues in contact with ILE 639 (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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641B LEU* 3.8 22.5 - - + +
626C PHE* 4.8 6.7 - - + -
635C THR* 3.4 26.6 + - + +
636C GLN* 5.0 1.8 - - - +
637C PHE 2.9 2.0 + - - -
638C ARG* 1.3 74.4 - - + +
640C ILE* 1.3 62.8 + - - +
641C LEU 2.9 1.8 - - - -
642C GLY* 2.5 26.7 + - - -
644C ILE* 3.3 29.2 - - + -
649C ILE* 4.6 19.7 - - + -
660C TYR* 5.3 9.4 - - + +
661C PHE* 4.5 17.7 - - + -
664C PHE* 4.2 25.8 - - + -
665C VAL* 5.2 2.0 - - + -
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Residues in contact with ILE 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 4.9 9.0 - - - +
604C PHE* 6.2 1.3 - - + -
608C PHE* 5.6 1.8 - - + -
636C GLN 3.9 9.9 - - - +
637C PHE* 2.9 30.3 - - + +
639C ILE* 1.3 78.6 - - - +
641C LEU* 1.3 61.3 + - + +
664C PHE* 4.5 14.8 - - + -
665C VAL* 6.1 1.1 - - - -
669C PHE* 4.2 28.8 - - + -
672C LEU* 3.3 43.1 - - + -
673C LEU* 5.8 0.2 - - + -
665D VAL* 6.5 0.9 - - + -
669D PHE* 4.2 27.8 - - + -
670D PHE* 4.9 6.7 - - + -
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Residues in contact with LEU 641 (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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641B LEU* 4.7 8.2 - - - +
637C PHE 3.1 11.9 + - - +
638C ARG* 3.5 11.2 - - + +
639C ILE 2.7 6.7 + - - -
640C ILE* 1.3 78.4 - - + +
642C GLY* 1.3 63.5 + - - +
643C ASP* 5.6 2.5 - - + -
639D ILE* 3.7 30.3 - - + +
640D ILE* 4.8 7.6 - - - +
641D LEU 4.6 8.2 - - - +
642D GLY* 3.7 27.7 - - - -
643D ASP 4.7 1.1 - - - +
644D ILE* 4.7 14.4 - - + -
661D PHE* 4.9 8.7 - - + -
665D VAL* 3.7 30.3 - - + -
669D PHE* 5.9 8.7 - - + -
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Residues in contact with GLY 642 (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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641B LEU* 3.8 15.5 - - - -
642B GLY* 6.1 0.7 - - - -
638C ARG 2.5 24.4 + - - +
639C ILE 2.5 16.5 + - - -
641C LEU* 1.3 80.8 - - - +
643C ASP* 1.3 71.0 + - - +
644C ILE* 2.9 16.5 + - - +
642D GLY* 6.1 0.9 - - - -
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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
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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) + - + + + + + -
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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