Contacts of the strand formed by residues 89 - 97 (chain B) in PDB entry 3IEU
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 VAL 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B PHE* 3.5 13.6 - - + +
12B ALA* 3.9 10.1 - - + +
61B VAL* 4.0 16.2 - - + -
63B THR 3.9 10.1 - - - +
64B PRO 3.2 33.9 - - - +
65B GLY* 4.2 7.6 - - - -
66B LEU* 4.3 12.0 - - + +
88B ASP* 1.3 76.4 - - - +
90B GLU* 1.3 62.3 + - - +
91B LEU 3.4 24.0 - - - +
92B VAL* 3.9 8.7 - - + -
116B LYS* 6.1 1.0 - - - +
117B ALA* 3.6 15.0 - - + +
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLY* 4.9 0.2 - - - -
10B PHE 2.8 17.8 + - - +
11B ILE* 4.8 2.9 - - + -
88B ASP* 3.4 21.0 + - - +
89B VAL* 1.3 74.8 - - - +
91B LEU* 1.3 63.1 + - + +
117B ALA* 4.2 4.9 - - - -
118B PRO* 3.4 16.2 - - - +
172B HIS* 3.5 31.1 - - + +
174B PRO* 3.6 35.1 - - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE 4.0 0.8 + - - -
11B ILE* 3.6 20.0 - - + -
12B ALA 3.0 24.4 + - - +
89B VAL* 3.4 5.2 - - - +
90B GLU* 1.3 81.1 - - - +
92B VAL* 1.3 74.4 + - - +
93B ILE* 4.6 4.9 - - + -
117B ALA* 4.1 0.8 - - - +
118B PRO* 3.5 19.5 - - + +
120B ILE* 3.8 24.2 - - + -
149B LEU* 4.7 0.7 - - + -
168B ILE* 4.1 9.9 - - + -
169B VAL* 3.8 43.3 - - + +
172B HIS* 4.2 25.1 - - + +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 3.8 11.0 - - + -
14B VAL* 3.5 31.9 - - + -
64B PRO* 4.2 13.9 - - + +
89B VAL* 3.9 15.7 - - + -
91B LEU* 1.3 79.3 - - - +
93B ILE* 1.3 61.4 + - - +
94B PHE 3.5 0.2 + - - -
112B LEU* 4.0 21.8 - - + -
117B ALA* 4.2 12.1 - - + +
118B PRO 2.9 15.8 + - - +
119B VAL* 3.4 11.8 - - + -
120B ILE* 2.8 31.0 + - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.0 13.9 - - + -
12B ALA 2.9 17.4 + - - +
13B ILE* 3.5 15.7 - - + -
14B VAL* 2.9 30.8 + - - +
24B LEU* 4.3 8.1 - - + -
28B LEU* 4.6 4.9 - - + -
60B TYR* 4.6 5.4 - - + -
91B LEU* 4.6 7.9 - - + -
92B VAL* 1.3 75.4 - - - +
94B PHE* 1.3 57.9 + - - +
95B VAL* 3.7 17.6 - - + +
120B ILE* 3.8 14.8 - - + -
122B ALA* 4.0 17.9 - - + -
165B ILE* 3.6 28.3 - - + -
169B VAL* 3.9 16.6 - - + -
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Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B VAL* 3.7 7.4 - - + -
15B GLY* 3.9 5.2 - - - -
16B ARG 5.2 0.2 - - - -
92B VAL 3.5 1.6 + - - -
93B ILE* 1.3 71.4 - - - +
95B VAL* 1.3 82.1 + - - +
96B VAL* 3.9 14.8 - - + -
101B TRP* 4.3 9.4 - + - -
105B ASP* 3.5 25.6 - - - -
108B VAL* 3.4 29.6 - - + -
109B LEU* 4.1 22.0 - - + -
112B LEU* 3.8 15.0 - - + -
119B VAL* 3.7 12.8 - - + -
120B ILE 2.7 17.7 + - - +
121B LEU* 3.3 25.1 - - + +
122B ALA* 2.8 27.9 + - - +
148B PHE* 4.3 11.9 - + - -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ILE* 4.1 14.6 - - + -
14B VAL 2.8 20.4 + - - +
15B GLY* 3.6 17.3 - - - -
19B VAL* 3.5 29.3 - - + +
20B GLY 4.8 1.8 - - - -
21B LYS* 4.4 7.9 - - + +
24B LEU* 4.2 13.0 - - + -
93B ILE* 3.7 22.0 - - + +
94B PHE* 1.3 80.9 - - - +
96B VAL* 1.3 71.6 + - - +
105B ASP* 4.6 1.0 - - - +
122B ALA* 3.4 11.7 - - + +
124B ASN* 4.0 19.7 - - + -
154B ILE* 5.5 0.4 - - + -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 4.1 7.9 - - - -
94B PHE* 3.9 21.8 - - + -
95B VAL* 1.3 79.2 - - - +
97B GLU* 1.3 62.0 + - - +
98B GLY 5.2 1.8 - - - +
100B ARG 4.9 5.2 - - - +
101B TRP* 4.2 15.5 - - + -
105B ASP* 3.3 24.0 - - - +
121B LEU* 3.9 17.3 - - + -
122B ALA 3.1 11.2 + - - +
123B VAL* 3.9 20.2 - - + -
124B ASN* 2.7 29.8 + - - +
138B HIS* 6.3 0.4 - - - +
142B LEU* 4.8 7.9 - - + -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG* 2.8 37.9 + - - +
18B ASN* 4.3 10.0 + - - +
19B VAL* 4.2 11.2 - - + +
96B VAL* 1.3 76.4 - - - +
98B GLY* 1.3 69.4 + - - +
100B ARG* 2.9 41.1 + - + +
105B ASP* 4.9 1.0 + - - -
124B ASN 3.6 2.2 - - - -
125B LYS* 3.2 43.4 + - + +
309B SO4 5.2 3.9 + - - -
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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