Contacts of the helix formed by residues 629 - 638 (chain C) in PDB entry 5UH8
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 GLY 629 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C ASN* 4.8 6.5 - - - -
30C ASN* 3.4 24.1 + - - +
38C ARG* 4.6 3.8 - - - -
584C ARG* 4.8 5.3 + - - -
628C THR* 1.3 78.5 - - - +
630C MET* 1.3 61.5 + - - +
631C GLU* 2.8 12.3 + - - -
632C LEU* 3.7 12.7 + - - +
633C ARG* 4.5 2.3 + - - +
712C GLU* 6.0 0.2 - - - -
973C SER* 3.3 16.8 + - - -
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Residues in contact with MET 630 (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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50C VAL* 4.3 18.2 - - + -
53C LEU* 5.7 1.3 - - - -
502C VAL* 4.2 25.4 - - + -
584C ARG* 4.1 30.9 - - + +
589C VAL* 4.0 33.0 - - + +
592C ALA* 3.6 25.8 - - + +
593C MET* 4.2 8.5 - - + -
628C THR* 3.2 17.5 + - - +
629C GLY* 1.3 73.9 - - - +
631C GLU* 1.3 65.3 + - - +
632C LEU 3.1 4.5 + - - -
633C ARG* 3.5 10.5 + - - +
634C ALA* 3.1 23.5 + - + +
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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
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38C ARG* 4.0 10.4 + - - +
593C MET* 4.1 17.4 - - + +
624C PRO* 4.4 18.6 - - + -
627C GLY* 3.1 12.2 - - - -
628C THR* 2.4 38.7 + - - +
629C GLY* 2.8 24.1 + - - -
630C MET* 1.3 78.8 - - - +
632C LEU* 1.3 61.3 + - - +
634C ALA 4.3 0.2 - - - -
635C ALA* 3.6 1.0 + - - +
712C GLU* 3.3 13.1 - - + +
713C MET* 2.7 54.4 + - + +
888C ARG* 4.6 5.2 + - - +
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Residues in contact with LEU 632 (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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30C ASN* 3.7 31.2 - - + +
33C PRO* 3.9 11.4 - - + -
35C ALA* 3.6 35.0 - - + -
36C PRO 5.9 0.4 - - - +
629C GLY 3.7 10.2 + - - +
630C MET 3.1 0.6 - - - -
631C GLU* 1.3 78.3 + - - +
633C ARG* 1.3 71.5 + - + +
634C ALA 3.1 0.9 + - - -
635C ALA 3.2 9.9 + - - -
636C ILE* 3.3 28.8 + - + +
701C VAL* 5.6 1.3 - - + -
710C ASP 5.1 1.1 - - - +
711C GLY* 3.3 31.3 - - - +
712C GLU* 4.1 16.5 + - + +
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Residues in contact with ARG 633 (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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30C ASN* 4.0 27.8 - - - +
32C VAL* 6.5 1.6 - - - -
33C PRO* 5.6 4.5 - - - -
49C GLU* 3.9 13.9 + - - +
50C VAL* 2.6 59.5 + - + +
51C PRO 3.6 6.9 + - - -
52C GLY* 4.5 1.2 - - - +
53C LEU* 4.2 2.4 - - + +
629C GLY 4.5 1.7 + - - +
630C MET* 3.5 14.7 + - - +
632C LEU* 1.3 87.8 - - + +
634C ALA* 1.3 62.0 + - - +
636C ILE* 4.0 10.4 - - - +
637C ASP* 3.0 60.9 + - - +
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Residues in contact with ALA 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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53C LEU* 4.3 10.7 - - - +
446C LEU* 5.0 2.9 - - + -
449C LEU* 4.0 8.5 - - + +
589C VAL* 4.4 20.4 - - + -
593C MET* 4.8 8.5 - - + -
630C MET* 3.1 21.7 + - + +
633C ARG* 1.3 75.4 - - - +
635C ALA* 1.3 65.2 + - - +
637C ASP 3.9 0.3 - - - -
638C ALA* 3.0 25.6 + - - +
713C MET* 3.8 18.3 - - + +
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Residues in contact with ALA 635 (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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445C PRO* 5.7 0.6 - - - +
631C GLU 3.6 1.5 + - - +
632C LEU 3.2 1.6 + - - -
634C ALA* 1.3 79.0 - - - +
636C ILE* 1.3 62.8 + - - +
638C ALA* 3.5 12.5 - - - +
639C GLY 4.2 0.7 + - - -
641C VAL* 3.4 18.4 + - - +
708C THR* 3.8 13.7 - - + +
711C GLY* 3.6 19.1 - - - +
712C GLU 3.8 3.1 - - - -
713C MET* 3.6 43.5 - - - +
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Residues in contact with ILE 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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33C PRO* 4.3 21.3 - - + -
632C LEU* 3.3 33.5 + - + +
633C ARG* 4.0 10.1 - - - +
634C ALA 3.2 0.6 - - - -
635C ALA* 1.3 78.2 - - - +
637C ASP* 1.3 72.9 + - - +
638C ALA 3.2 0.9 + - - -
639C GLY* 3.3 12.3 + - - -
641C VAL* 3.9 10.7 - - + +
643C VAL* 3.9 29.5 - - + +
699C GLY 4.8 4.3 - - - +
701C VAL* 3.8 25.8 - - + -
711C GLY 4.3 4.3 - - - +
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Residues in contact with ASP 637 (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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52C GLY* 3.9 3.6 - - - -
53C LEU* 3.2 47.3 + - + +
54C LEU* 3.2 27.9 - - + +
449C LEU* 4.7 1.8 - - + -
633C ARG* 3.0 47.9 + - - +
634C ALA 4.2 0.4 - - - +
636C ILE* 1.3 81.0 - - - +
638C ALA* 1.3 64.6 + - - +
639C GLY* 3.1 1.5 + - - -
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Residues in contact with ALA 638 (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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54C LEU* 4.7 2.5 - - - +
163C LYS* 4.7 1.9 - - - +
445C PRO* 4.1 37.1 - - + +
446C LEU* 5.0 0.4 - - - +
449C LEU* 4.6 16.1 + - + +
452C LYS* 4.0 17.3 + - - -
634C ALA 3.0 18.3 + - - +
635C ALA* 3.5 10.5 - - - +
636C ILE 3.1 0.8 - - - -
637C ASP* 1.3 77.8 - - - +
639C GLY* 1.3 58.6 + - - +
640C ASP* 3.1 14.7 + - + +
713C MET* 5.3 0.4 - - - -
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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
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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