Contacts of the helix formed by residues 75 - 83 (chain A) in PDB entry 4Q96
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 PRO 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LYS* 5.8 0.7 - - + -
74A GLY* 1.3 83.4 - - - +
76A GLU* 1.3 70.4 + - - +
77A PHE 3.4 0.9 - - - -
78A THR* 3.3 9.7 + - - +
79A ARG* 2.9 56.8 + - + +
201A UNX 3.7 25.1 - - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 5.2 6.5 - - + +
37A ALA* 4.7 12.8 - - + -
74A GLY* 3.3 10.8 - - - -
75A PRO* 1.3 93.2 - - - +
77A PHE* 1.3 59.6 + - + +
79A ARG* 3.2 32.8 + - - +
80A GLU* 2.7 35.3 + - + +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.5 29.2 - - + -
31A ILE* 4.4 1.8 - - + -
34A ARG* 3.6 24.0 - - + -
37A ALA* 3.8 20.6 - - + -
40A ILE* 3.7 39.5 - - + -
41A VAL* 4.2 3.8 - - + -
66A VAL* 3.6 28.0 - - + +
67A ILE* 4.8 2.5 - - - -
70A SER* 3.5 28.0 - - - +
74A GLY 4.6 2.0 + - - -
75A PRO 3.4 0.2 - - - -
76A GLU* 1.3 75.6 - - + +
78A THR* 1.3 66.4 + - - +
80A GLU* 4.3 2.0 - - - +
81A PHE* 2.8 54.1 + + + -
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 3.8 11.6 + - - +
70A SER* 4.5 2.9 + - - -
71A LYS* 3.3 43.3 + - - +
75A PRO* 3.3 17.5 + - + +
76A GLU 3.3 0.2 - - - -
77A PHE* 1.3 79.5 - - - +
79A ARG* 1.3 59.4 + - + +
82A GLU* 2.9 22.5 + - - +
117B TYR* 2.9 46.0 + - + -
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PRO* 2.9 43.2 + - + +
76A GLU* 3.2 40.6 + - - +
78A THR* 1.3 77.4 - - + +
80A GLU* 1.3 72.1 + - + +
82A GLU* 3.3 20.1 + - - +
83A SER* 3.5 11.1 + - - -
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 4.0 8.1 - - + +
38A GLY* 3.6 36.0 + - - +
41A VAL* 3.6 31.9 - - + +
76A GLU* 2.7 24.7 + - + +
77A PHE* 4.0 3.8 - - - +
79A ARG* 1.3 78.6 + - + +
81A PHE* 1.3 59.9 + - - +
83A SER* 2.9 27.8 + - - -
84A VAL 4.2 0.5 + - - -
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 6.3 1.6 - - + -
40A ILE* 5.5 2.5 - - + -
41A VAL* 3.7 19.3 - - + -
44A TRP* 3.7 47.6 - + + -
62A LEU* 6.3 0.4 - - + -
63A ALA* 3.7 26.7 - - + -
66A VAL* 4.1 16.4 - - + -
67A ILE* 3.5 21.1 - - + -
77A PHE* 2.8 48.8 + + - +
80A GLU* 1.3 74.2 - - - +
82A GLU* 1.3 66.6 + - - +
83A SER 3.0 2.7 - - - -
84A VAL* 3.0 6.5 + - + +
85A LEU* 3.0 32.9 + - + +
117B TYR* 3.5 12.8 - - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A THR* 2.9 21.8 + - - +
79A ARG* 3.3 14.7 + - - +
81A PHE* 1.3 76.2 - - - +
83A SER* 1.3 60.9 + - - +
84A VAL 3.4 0.5 + - - -
85A LEU* 4.0 1.6 + - - -
86A VAL* 5.0 1.0 + - - +
117B TYR* 3.6 26.6 + - + -
121B PHE* 3.5 50.1 - - + +
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Residues in contact with SER 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG 3.5 7.4 + - - -
80A GLU* 2.9 26.0 + - - -
81A PHE 3.0 1.6 + - - -
82A GLU* 1.3 79.2 - - - +
84A VAL* 1.3 68.9 + - - +
86A VAL 5.5 0.2 - - - -
87A ASP* 5.4 2.8 - - - +
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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
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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