Contacts of the helix formed by residues 69 - 78 (chain A) in PDB entry 6I3N
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 ASP 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ARG* 5.0 1.4 - - - +
31A ARG* 5.9 2.8 - - - +
34A SER* 2.8 35.3 + - - -
38A ASN* 3.7 10.8 + - - +
68A ALA* 1.3 78.0 - - + +
70A PRO* 1.3 69.8 - - - +
71A THR 3.7 0.7 + - - -
72A GLY* 3.1 18.2 + - - -
73A ARG* 3.3 27.9 + - - +
63B GLN* 5.8 3.7 - - - +
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Residues in contact with PRO 70 (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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38A ASN* 3.8 19.1 - - + +
47A TRP* 3.5 39.2 - - + +
64A LEU* 3.3 23.5 - - - +
65A GLU* 4.6 5.8 - - - +
67A GLN 3.6 13.9 - - - +
68A ALA* 4.0 0.9 - - - -
69A ASP* 1.3 84.7 - - - +
71A THR* 1.3 60.5 + - - +
73A ARG* 4.1 4.8 - - + +
74A LEU* 2.9 29.3 + - - +
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Residues in contact with THR 71 (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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33A LEU* 4.1 17.3 - - + +
34A SER* 3.8 17.0 - - - +
37A LEU* 3.9 19.7 - - + -
38A ASN* 3.5 28.4 + - - +
47A TRP* 3.6 15.0 - - + +
50A LEU* 5.6 4.3 - - + -
69A ASP* 3.2 1.7 - - - -
70A PRO* 1.3 76.6 - - - +
72A GLY* 1.3 58.5 + - - +
74A LEU* 3.3 9.6 + - + +
75A LEU* 2.9 38.5 + - + +
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Residues in contact with GLY 72 (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 ARG* 4.7 15.0 + - - -
34A SER* 3.9 4.2 + - - -
69A ASP* 3.1 27.2 + - - -
70A PRO 3.4 0.2 - - - -
71A THR* 1.3 77.3 - - - +
73A ARG* 1.3 63.3 + - - +
75A LEU* 3.3 6.5 + - - +
76A ASP* 2.9 36.3 + - - +
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Residues in contact with ARG 73 (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 ARG* 6.0 2.2 - - - +
64A LEU* 3.9 10.5 - - + +
67A GLN* 3.4 45.5 - - + +
68A ALA 4.0 5.3 + - - +
69A ASP* 3.3 38.3 + - - +
70A PRO* 4.1 3.4 - - + +
72A GLY* 1.3 79.2 + - - +
74A LEU* 1.3 60.5 + - - +
76A ASP* 2.5 35.1 + - - +
77A ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 74 (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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47A TRP* 3.6 38.6 - - + +
50A LEU* 4.5 8.7 - - + -
51A ALA* 3.7 17.5 - - + +
54A MET* 3.6 21.1 - - + -
56A PHE* 3.6 27.1 - - + -
64A LEU* 3.7 20.8 - - + +
70A PRO 2.9 18.4 + - - +
71A THR* 3.4 9.0 - - + +
73A ARG* 1.3 75.9 - - - +
75A LEU* 1.3 61.1 + - + +
77A ALA* 3.4 2.0 + - - -
78A TRP* 3.0 29.6 + - - +
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Residues in contact with LEU 75 (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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22A LEU* 3.7 23.8 - - + +
25A LEU* 5.4 2.2 - - + -
30A ARG* 3.4 42.6 - - + +
33A LEU* 4.0 23.3 - - + -
50A LEU* 5.5 5.4 - - + -
54A MET* 5.5 1.6 - - + -
71A THR* 2.9 29.4 + - + +
72A GLY 3.3 2.9 + - - +
74A LEU* 1.3 78.4 - - + +
76A ASP* 1.3 64.2 + - - +
78A TRP* 3.4 9.7 + - + +
79A GLN* 3.2 28.2 + - - +
89A LEU* 4.2 23.3 - - + -
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Residues in contact with ASP 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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30A ARG* 3.9 16.7 + - - -
72A GLY 2.9 15.7 + - - +
73A ARG* 2.5 44.9 + - - +
74A LEU 3.3 0.2 - - - -
75A LEU* 1.3 78.1 - - - +
77A ALA* 1.3 61.0 + - - +
79A GLN* 3.3 27.3 + - + +
80A GLY 4.7 0.3 + - - -
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Residues in contact with ALA 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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56A PHE* 4.0 21.4 - - + -
64A LEU* 5.0 10.1 - - + -
73A ARG 2.9 18.3 + - - +
74A LEU* 3.7 5.8 - - - +
76A ASP* 1.3 76.2 - - - +
78A TRP* 1.3 57.2 + - - +
79A GLN 3.3 1.9 + - - -
80A GLY 4.4 3.9 + - - +
81A ARG* 3.7 15.8 - - - +
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Residues in contact with TRP 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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22A LEU* 3.7 34.3 - - + +
54A MET* 3.4 56.1 + - + +
56A PHE* 4.0 11.2 - + + -
74A LEU 3.0 16.4 + - - +
75A LEU* 3.4 10.7 + - + +
76A ASP 3.2 0.4 - - - -
77A ALA* 1.3 78.2 - - - +
79A GLN* 1.3 63.7 + - - +
80A GLY 3.6 0.4 - - - -
81A ARG* 3.6 26.8 - - + +
83A GLY 4.4 2.6 - - - +
84A ALA* 3.2 32.1 - - + +
85A SER 3.8 11.0 - - - -
88A ARG* 3.7 31.4 - - + -
89A LEU* 3.9 21.8 - - + -
92A LEU* 4.2 3.8 - - + -
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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