Contacts of the strand formed by residues 92 - 101 (chain A) in PDB entry 3IEQ
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 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A GLY 4.2 0.6 + - - -
91A PHE* 1.3 73.7 - - - +
93A ILE* 1.3 63.9 + - - +
94A ARG* 3.7 2.6 + - - +
156A VAL* 3.3 6.2 - - - +
157A VAL* 3.0 45.8 + - + +
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Residues in contact with ILE 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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50A LEU* 3.8 34.8 - - + -
83A ALA* 4.2 15.9 - - + +
86A VAL* 4.5 9.6 - - + -
91A PHE 5.4 0.4 - - - +
92A ALA* 1.3 76.9 - - - +
94A ARG* 1.3 66.7 + - - +
95A ASN 4.0 11.2 - - - +
96A VAL* 4.3 4.0 - - + -
122A LEU* 3.9 36.8 - - + +
124A LEU* 3.4 39.5 - - + +
128A ARG* 5.3 0.7 + - - -
155A LEU 3.9 10.3 - - - +
156A VAL* 4.1 6.7 - - + -
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Residues in contact with ARG 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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3A PHE* 3.6 22.7 - - + -
92A ALA* 3.7 3.7 + - - +
93A ILE* 1.3 78.2 - - - +
95A ASN* 1.3 62.7 + - - +
124A LEU* 4.9 0.9 - - - -
128A ARG* 2.9 47.5 + - - +
155A LEU* 2.8 31.5 + - + +
156A VAL 4.6 1.8 - - - -
157A VAL* 3.4 40.4 - - + +
1C MET 3.4 27.7 + - - +
2C ASP* 4.3 9.5 + - - +
3C PHE 4.2 5.7 - - - +
4C ARG* 4.9 0.4 - - - -
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Residues in contact with ASN 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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93A ILE* 3.9 3.4 - - - +
94A ARG* 1.3 81.4 - - - +
96A VAL* 1.3 76.9 + - - +
97A ASP* 4.2 1.4 - - - +
124A LEU* 4.8 1.1 - - - -
128A ARG* 3.3 17.2 + - - +
154A ALA* 3.4 4.0 - - - +
155A LEU* 3.0 40.0 + - - +
4C ARG* 3.2 28.0 - - - +
5C ILE* 2.9 48.8 + - - +
52C GLY 4.7 2.2 + - - -
53C ALA 4.5 4.0 + - - -
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Residues in contact with VAL 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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46A ILE* 4.0 36.6 - - + -
50A LEU* 4.5 1.8 - - + -
93A ILE* 4.3 7.6 - - + -
95A ASN* 1.3 85.9 + - - +
97A ASP* 1.3 73.9 + - - +
118A ILE* 4.8 4.5 - - + -
122A LEU* 3.7 28.7 - - + -
124A LEU* 4.9 1.3 - - + -
128A ARG 3.0 9.4 + - - +
129A VAL* 3.5 12.1 - - + -
130A ASN* 2.9 26.7 + - - +
152A ALA* 5.3 0.7 - - + -
153A ALA 3.4 6.7 - - - +
154A ALA* 4.2 14.4 - - + -
52C GLY 5.0 0.2 - - - +
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Residues in contact with ASP 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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95A ASN* 4.2 1.0 - - - +
96A VAL* 1.3 76.8 - - - +
98A SER* 1.3 71.1 + - - +
130A ASN* 3.0 24.7 + - - +
132A LYS* 2.7 34.1 + - - -
152A ALA* 3.3 2.4 - - - +
153A ALA* 2.8 33.8 + - + +
5C ILE 3.8 19.3 - - - +
6C GLY* 4.0 2.2 - - - -
7C GLN* 2.9 26.6 + - + +
52C GLY* 3.3 22.3 - - - +
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Residues in contact with SER 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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42A LEU* 3.5 27.0 - - - +
46A ILE* 4.3 8.0 - - - +
96A VAL* 5.0 0.4 - - - +
97A ASP* 1.3 82.4 + - - +
99A THR* 1.3 57.1 + - - +
130A ASN 3.0 14.5 + - - -
131A VAL* 3.5 11.5 - - - +
132A LYS* 2.8 34.1 + - - +
151A GLN 3.1 16.4 - - - -
152A ALA* 4.2 5.4 - - - -
7C GLN* 3.2 8.7 - - - -
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Residues in contact with THR 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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42A LEU* 4.8 0.2 - - - +
98A SER* 1.3 71.2 - - - +
100A ILE* 1.3 74.4 + - - +
101A ILE* 4.2 9.2 + - + +
132A LYS* 3.2 31.0 + - + +
133A ALA 4.8 0.2 - - - +
134A LYS* 3.8 30.5 - - + -
150A ALA* 3.1 6.1 - - - +
151A GLN* 2.8 44.1 + - - +
7C GLN* 2.7 24.6 + - - -
9C TYR* 4.9 6.1 + - + -
48C ASP* 4.9 1.0 + - - +
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Residues in contact with ILE 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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22A ILE* 3.8 19.5 - - + -
41A VAL* 5.2 1.6 - - + -
42A LEU* 4.0 17.5 - - + -
99A THR* 1.3 78.8 - - - +
101A ILE* 1.3 66.4 + - - +
102A ALA 3.9 0.2 + - - -
107A LEU* 3.6 25.7 - - + +
111A ILE* 4.1 9.6 - - + -
114A MET* 3.7 32.1 - - + -
131A VAL* 3.8 15.3 - - + -
132A LYS 2.8 11.9 + - - +
133A ALA* 3.4 1.1 - - - +
134A LYS 2.9 26.5 + - - +
148A ILE* 3.7 25.1 - - + -
149A GLU 3.4 4.5 - - - +
150A ALA* 4.9 1.3 - - + -
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Residues in contact with ILE 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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99A THR* 4.2 7.4 - - + +
100A ILE* 1.3 76.3 - - - +
102A ALA* 1.3 65.2 + - - +
134A LYS* 3.3 10.5 - - + +
135A THR 3.8 2.7 - - - +
136A ASN* 3.6 43.7 - - + +
142A LEU* 3.9 18.0 - - + +
148A ILE* 3.5 5.9 - - - +
149A GLU* 2.8 68.1 + - + +
151A GLN* 3.6 22.2 - - + +
9C TYR* 3.8 19.1 - - + -
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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