Contacts of the strand formed by residues 92 - 101 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90C GLY 4.2 0.2 + - - -
91C PHE* 1.3 74.4 - - - +
93C ILE* 1.3 66.0 + - - +
94C ARG* 3.6 2.6 + - - +
156C VAL* 3.3 4.2 - - - +
157C VAL* 2.8 46.2 + - + +
158C ARG 6.3 0.2 - - - -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 3.7 35.4 - - + -
83C ALA* 4.5 15.0 - - + +
86C VAL* 4.4 15.5 - - + -
91C PHE 5.6 0.2 - - - +
92C ALA* 1.3 74.9 - - - +
94C ARG* 1.3 66.3 + - - +
95C ASN 4.1 4.7 - - - +
96C VAL* 4.3 8.7 - - + -
122C LEU* 3.9 34.8 - - + +
124C LEU* 3.4 41.9 - - + +
128C ARG* 5.3 0.7 - - - -
155C LEU 4.0 8.7 - - - +
156C VAL* 4.2 2.9 - - + -
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 3.1 26.1 + - - +
2B ASP* 4.0 13.5 + - - +
3B PHE 4.3 5.2 - - - +
1C MET* 3.6 35.2 - - - +
3C PHE* 3.4 21.7 - - + -
92C ALA* 3.6 3.4 + - - +
93C ILE* 1.3 78.0 - - - +
95C ASN* 1.3 60.8 + - - +
124C LEU* 4.4 1.1 - - - +
128C ARG* 2.9 53.4 + - - +
155C LEU* 2.8 33.4 + - + +
156C VAL 4.6 0.4 - - - -
157C VAL* 3.6 27.8 - - + +
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Residues in contact with ASN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ARG* 3.3 26.7 - - - +
5B ILE* 2.8 49.1 + - - +
52B GLY 4.7 2.2 + - - -
53B ALA 4.4 4.4 + - - -
55B ALA* 6.4 0.2 - - - +
93C ILE* 3.8 4.2 - - - +
94C ARG* 1.3 81.6 - - - +
96C VAL* 1.3 76.0 + - - +
97C ASP* 4.6 1.2 - - - +
124C LEU* 4.9 0.9 - - - -
128C ARG* 3.2 16.3 + - + +
154C ALA* 3.4 3.1 - - - +
155C LEU* 3.0 47.9 + - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY 5.0 0.2 - - - +
55B ALA* 5.9 0.2 - - - +
46C ILE* 3.8 39.0 - - + -
50C LEU* 4.2 9.6 - - + -
93C ILE* 4.3 3.6 - - + -
95C ASN* 1.3 84.3 + - - +
97C ASP* 1.3 70.8 + - - +
118C ILE* 4.9 4.7 - - + -
122C LEU* 3.9 26.2 - - + -
124C LEU* 5.0 1.1 - - + +
128C ARG 2.9 9.2 + - - +
129C VAL* 3.5 9.5 - - + -
130C ASN* 2.9 28.3 + - - +
152C ALA* 5.3 0.4 - - + -
153C ALA 3.4 5.8 - - - +
154C ALA* 4.1 15.7 - - + -
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Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE 3.8 17.9 - - - +
6B GLY* 3.4 2.6 - - - -
7B GLN* 2.9 24.2 + - + +
52B GLY* 3.2 22.2 - - - +
95C ASN* 4.3 0.6 - - - +
96C VAL* 1.3 76.3 - - - +
98C SER* 1.3 71.9 + - - +
130C ASN* 3.0 31.1 + - - +
132C LYS* 2.9 20.8 + - - -
152C ALA* 3.3 2.8 - - - +
153C ALA* 2.8 34.1 + - + +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 3.3 9.9 - - - -
42C LEU* 3.5 25.6 - - - +
46C ILE* 4.2 8.4 - - - +
97C ASP* 1.3 81.1 + - - +
99C THR* 1.3 60.2 + - - +
130C ASN 2.9 15.0 + - - -
131C VAL* 3.6 11.3 - - - +
132C LYS* 2.9 33.1 + - - +
151C GLN 3.1 14.8 - - - -
152C ALA* 4.2 6.7 - - - -
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Residues in contact with THR 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B GLN* 2.7 23.4 + - - -
9B TYR* 4.7 12.6 + - + +
48B ASP* 5.3 0.6 + - - +
98C SER* 1.3 71.5 - - - +
100C ILE* 1.3 71.9 + - - +
101C ILE* 4.1 9.3 + - + +
132C LYS* 3.0 28.0 + - + +
134C LYS* 3.7 30.3 - - + -
150C ALA* 3.2 6.1 - - - +
151C GLN* 2.9 42.9 + - - +
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Residues in contact with ILE 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.8 16.8 - - + -
41C VAL* 5.1 2.9 - - + -
42C LEU* 3.8 19.7 - - + -
99C THR* 1.3 76.7 - - - +
101C ILE* 1.3 63.4 + - - +
102C ALA* 3.7 1.1 + - + -
107C LEU* 3.6 27.8 - - + +
111C ILE* 5.0 2.5 - - + -
114C MET* 3.5 34.3 - - + -
131C VAL* 3.7 15.3 - - + -
132C LYS 2.8 16.1 + - - +
133C ALA* 3.3 3.9 - - + +
134C LYS 2.9 27.2 + - - +
148C ILE* 3.8 24.0 - - + -
149C GLU 3.6 3.6 - - - +
150C ALA* 4.5 0.7 - - + +
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 3.5 33.7 - - + -
99C THR* 4.3 9.9 - - + +
100C ILE* 1.3 71.7 - - - +
102C ALA* 1.3 61.3 + - - +
134C LYS* 3.3 2.9 - - + +
135C THR 3.9 13.2 - - - +
136C ASN* 3.5 30.7 - - + +
142C LEU* 3.6 19.6 - - + +
147C GLY 4.5 0.2 - - - +
148C ILE* 3.5 7.4 - - - +
149C GLU* 2.7 68.3 + - + +
151C GLN* 3.6 11.2 - - - +
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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