Contacts of the strand formed by residues 91 - 100 (chain A) in PDB entry 6I4X
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A LYS* 3.9 6.3 - - - +
88A THR* 2.7 40.4 + - - +
89A SER 3.3 1.8 + - - -
90A ALA* 1.3 78.8 - - - +
92A PRO* 1.3 77.5 - - - +
93A THR* 3.6 2.6 + - - +
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Residues in contact with PRO 92 (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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58A ALA 4.8 0.7 - - - +
59A LYS* 3.7 40.4 - - + +
62A LEU* 3.6 37.9 - - + +
63A LYS* 4.0 7.2 - - + +
86A VAL 3.5 8.3 - - - +
87A LYS* 3.9 6.0 - - + -
91A GLY* 1.3 86.7 - - - +
93A THR* 1.3 59.5 + - - +
94A ASN* 5.1 2.4 + - - +
-1D GLU* 5.1 3.8 - - - +
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Residues in contact with THR 93 (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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85A SER* 3.3 3.6 - - - -
86A VAL* 2.9 52.7 + - + +
88A THR* 3.8 17.7 - - + +
91A GLY 4.5 1.8 - - - +
92A PRO* 1.3 75.5 - - - +
94A ASN* 1.3 81.0 + - - +
95A LEU* 6.3 0.7 - - + -
-1D GLU 3.7 9.0 + - - -
1D THR* 2.4 31.5 + - + +
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Residues in contact with ASN 94 (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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55A VAL* 3.6 21.0 + - - +
58A ALA* 4.5 3.6 - - - +
73A ARG* 2.8 18.1 + - - +
83A THR* 4.0 0.7 - - + -
84A ILE 3.2 6.1 - - - +
85A SER* 2.5 28.9 + - - -
86A VAL* 5.9 0.2 - - - -
92A PRO* 5.1 1.6 + - - +
93A THR* 1.3 88.9 + - - +
95A LEU* 1.3 61.4 + - - +
-1D GLU* 3.0 25.3 + - - +
0D PTR 3.5 27.1 - - + -
1D THR* 2.7 33.0 + - - +
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Residues in contact with LEU 95 (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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83A THR* 4.2 1.5 - - - +
84A ILE* 2.7 47.6 + - + +
86A VAL* 5.8 2.5 - - + -
93A THR* 6.3 0.4 - - + -
94A ASN* 1.3 76.2 - - - +
96A ARG* 1.3 72.9 + - - +
106A LEU* 4.0 28.3 - - + -
107A ASP* 3.6 27.4 - - + +
150A LEU* 4.2 22.7 - - + -
0D PTR 4.8 0.4 - - - -
1D THR* 3.4 23.3 - - + +
3D LEU* 3.5 26.2 - - + -
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Residues in contact with ARG 96 (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 SER* 3.7 6.4 + - - -
77A HIS* 3.8 23.0 - - - +
80A TYR* 3.4 45.8 - - + -
82A LEU 3.7 4.9 - - - +
83A THR* 3.4 14.1 - - - +
95A LEU* 1.3 82.8 - - - +
97A ILE* 1.3 61.4 + - - +
106A LEU* 4.0 0.5 - - - -
107A ASP* 3.0 39.3 + - - +
-3D SER 4.2 9.3 - - - +
0D PTR 2.9 69.7 + - + +
1D THR 4.8 1.0 + - - -
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Residues in contact with ILE 97 (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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72A ILE* 3.7 14.4 - - + -
80A TYR* 3.5 15.8 - - - +
81A LEU* 4.3 7.3 + - - +
82A LEU* 3.0 27.4 + - + +
84A ILE* 3.6 38.8 - - + -
95A LEU 4.4 0.2 - - - +
96A ARG* 1.3 76.4 - - - +
98A GLU* 1.3 64.0 + - - +
99A TYR* 4.0 1.0 + - - +
104A PHE* 3.7 31.3 - - + -
105A ARG 3.5 17.0 - - - +
106A LEU* 4.7 2.9 - - + -
122A VAL* 3.6 22.7 - - + -
125A LEU* 4.1 7.2 - - + -
126A ILE* 4.5 3.4 - - + -
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Residues in contact with GLU 98 (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 ASP 5.6 2.5 - - - +
80A TYR* 4.1 22.4 - - + +
96A ARG 4.1 1.4 + - - -
97A ILE* 1.3 74.7 - - - +
99A TYR* 1.3 67.2 + - - +
100A GLN* 4.0 20.1 - - - +
103A LYS 3.5 1.4 - - - +
104A PHE* 3.3 6.5 - - - -
105A ARG* 2.8 62.4 + - + +
106A LEU 5.1 2.9 - - - +
107A ASP* 4.7 9.3 - - - +
114A SER* 5.1 4.0 + - - -
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Residues in contact with TYR 99 (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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32A GLN* 3.2 38.7 + - - +
35A ARG* 4.9 1.9 - - - +
36A LEU* 3.4 40.6 + - + +
79A ASP 5.8 1.2 + - - -
80A TYR* 6.2 0.8 - - - +
81A LEU* 4.6 17.0 - - + +
97A ILE 4.0 1.5 + - - +
98A GLU* 1.3 76.8 - - - +
100A GLN* 1.3 59.5 + - - +
102A GLY* 3.3 34.3 + - - -
103A LYS 3.6 6.5 - - - -
104A PHE* 3.4 48.5 - + + -
120A ASP 5.2 1.3 - - - -
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Residues in contact with GLN 100 (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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98A GLU* 4.0 19.2 - - - +
99A TYR* 1.3 75.0 - - - +
101A ASP* 1.3 75.9 + - + +
102A GLY 3.2 1.3 - - - -
103A LYS* 3.2 19.0 + - - +
105A ARG* 3.5 19.5 + - - +
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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