Contacts of the strand formed by residues 94 - 101 (chain A) in PDB entry 4I6H
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 ALA 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LYS* 3.8 6.4 - - - +
91A GLY* 2.9 40.6 + - - +
92A GLY 4.2 1.4 + - - +
93A PHE* 1.3 79.6 - - - +
95A LYS* 1.3 61.2 + - - +
96A CYS* 3.8 11.9 - - - -
111A LYS* 3.6 42.0 - - + -
112A ILE 4.1 0.4 - - - +
113A ILE* 4.0 9.7 - - + +
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Residues in contact with LYS 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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89A GLY 4.3 4.0 - - - +
90A LYS* 5.3 3.1 - - + +
93A PHE 3.5 3.3 + - - +
94A ALA* 1.3 72.7 - - - +
96A CYS* 1.3 61.4 + - - +
97A TYR* 3.8 29.5 + - + +
110A ALA 3.7 0.3 - - - +
112A ILE* 2.8 47.0 + - + +
114A PRO* 5.1 13.7 - - + -
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Residues in contact with CYS 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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87A THR* 3.4 7.8 + - - -
88A LEU* 2.5 32.6 + - + -
89A GLY 3.3 17.5 + - - +
91A GLY* 4.5 3.4 - - - -
94A ALA* 3.8 23.1 - - - -
95A LYS* 1.3 76.8 - - - +
97A TYR* 1.3 58.7 + - - +
110A ALA 3.3 8.5 - - - +
401A 1C8 3.4 59.9 - - + -
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Residues in contact with TYR 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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84A ARG* 3.4 55.5 + - + -
85A GLY 4.2 4.3 - - - +
86A LYS 3.2 7.9 - - - +
87A THR* 3.6 31.4 - - - -
88A LEU* 3.9 8.0 - - - +
95A LYS* 3.8 42.6 + - + +
96A CYS* 1.3 75.0 - - - +
98A GLU* 1.3 61.7 + - - +
110A ALA* 2.9 32.3 + - - +
112A ILE* 3.5 26.9 - - + -
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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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84A ARG* 3.5 6.6 - - - +
85A GLY* 2.6 33.5 + - - -
86A LYS* 2.7 48.0 + - - +
88A LEU* 3.8 18.8 - - + +
97A TYR* 1.3 72.5 - - - +
99A MET* 1.3 58.2 + - - +
100A THR* 4.2 0.7 - - - +
107A VAL* 3.9 17.0 - - + +
108A TYR 3.5 6.7 - - - +
161A TYR* 3.0 30.4 + - + -
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Residues in contact with MET 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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73A ILE* 3.7 27.1 - - + -
82A TYR* 3.8 22.0 - - + -
83A SER 3.5 4.5 - - - +
84A ARG* 4.9 1.1 - - - -
97A TYR 5.2 0.2 - - - -
98A GLU* 1.3 74.7 - - - +
100A THR* 1.3 64.5 + - - +
101A ASP 3.7 0.2 + - - -
107A VAL* 4.2 0.4 - - - +
108A TYR* 2.9 41.3 + - - +
110A ALA* 3.7 30.7 - - + -
112A ILE* 4.5 4.3 - - - -
149A PHE* 3.5 34.8 - - + -
156A TYR* 3.5 23.8 - - + -
158A LEU* 3.7 16.7 - - + +
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Residues in contact with THR 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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82A TYR* 3.1 8.7 - - - +
83A SER* 2.8 51.8 + - - -
98A GLU* 5.6 0.3 - - - +
99A MET* 1.3 69.7 - - - +
101A ASP* 1.3 74.0 + - - +
102A LEU* 3.6 13.9 + - + +
105A ASN* 4.6 7.9 - - - +
106A LYS 3.5 17.3 - - - +
107A VAL* 3.7 22.5 - - + +
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Residues in contact with ASP 101 (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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80A LYS* 3.0 28.6 + - - +
81A ARG 4.3 3.1 - - - +
82A TYR* 3.9 19.8 - - + -
99A MET 3.7 3.0 + - - -
100A THR* 1.3 72.9 - - - +
102A LEU* 1.3 65.2 + - - +
103A THR* 3.1 9.5 + - - -
104A ASN* 3.3 20.4 + - + +
105A ASN* 2.7 32.4 + - - -
106A LYS 3.0 8.7 + - - +
108A TYR* 3.9 12.8 - - + -
146A TYR* 2.4 33.7 + - + -
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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