Contacts of the strand formed by residues 93 - 101 (chain B) in PDB entry 3B94
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 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN 3.6 1.2 + - - -
92B ASN* 1.3 77.2 - - - +
94B LEU* 1.3 61.8 + - - -
95B TYR* 3.5 11.2 - - - -
141B GLU* 3.4 7.5 - - - +
142B LEU 2.9 31.0 + - - +
169B LEU* 3.9 3.1 - - - -
171B ALA 3.4 11.0 - - - -
172B ASN* 4.1 5.6 - - - -
173B PRO* 5.3 1.8 - - - -
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Residues in contact with LEU 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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59A MET* 5.0 5.4 - - - -
98A TYR* 3.7 44.6 - - + +
168A ILE* 4.3 21.3 - - + -
93B GLY* 1.3 73.1 - - - -
95B TYR* 1.3 53.9 + - - +
139B THR* 3.7 21.3 - - + -
140B TYR 3.6 11.7 - - - +
141B GLU* 4.2 6.5 - - + +
169B LEU* 3.6 2.3 - - - +
170B LEU* 2.7 63.2 + - + +
171B ALA* 2.7 21.9 + - + +
172B ASN* 4.7 0.2 - - - +
173B PRO* 4.9 6.6 - - + +
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B CYS* 3.6 33.3 + - - +
79B VAL* 4.3 4.3 - - + -
89B ILE* 3.8 6.2 - - + +
91B GLN* 2.5 33.6 + - - +
93B GLY 3.5 20.0 - - - -
94B LEU* 1.3 75.1 - - - +
96B LEU* 1.3 61.7 + - - +
97B ILE* 3.9 1.5 + - + -
139B THR* 3.6 3.3 - - - +
140B TYR* 2.6 39.4 + - - +
142B LEU* 3.7 34.1 - - + -
167B ILE* 3.5 26.5 - - + -
168B ILE 3.4 4.0 - - - -
169B LEU* 3.4 40.7 - - + +
170B LEU* 4.6 3.8 - - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.8 17.7 - - + -
95B TYR* 1.3 73.2 - - - +
97B ILE* 1.3 76.4 + - - +
98B TYR* 4.0 2.9 + - + -
138B GLY* 3.8 6.5 - - - +
139B THR* 3.4 21.1 - - - +
167B ILE* 3.6 2.2 - - - -
168B ILE* 2.7 53.3 + - + +
170B LEU* 4.0 13.2 - - + +
96C LEU* 4.6 8.3 - - + -
139C THR* 3.5 40.8 - - + +
170C LEU* 4.7 6.7 - - + -
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Residues in contact with ILE 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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95B TYR 3.9 1.1 + - - +
96B LEU* 1.3 83.5 - - - +
98B TYR* 1.3 67.5 + - - +
117B LEU* 4.0 16.2 - - + -
124B ILE* 4.7 2.2 - - + -
135B ASN* 5.5 0.5 + - - -
136B VAL* 3.6 3.9 - - + +
137B GLY* 3.3 17.8 - - - +
138B GLY 2.7 38.3 + - - +
140B TYR* 4.0 20.0 - - + -
142B LEU* 4.6 7.6 - - + -
148B ILE* 3.8 36.3 - - + -
165B TRP* 4.2 11.0 - - + -
166B GLY 3.5 9.2 - - - +
167B ILE* 4.1 19.3 - - + -
139C THR* 5.2 1.0 - - - -
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Residues in contact with TYR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B MET* 3.4 19.0 - - + +
60B ALA 3.3 12.5 + - - -
61B LYS* 3.7 13.0 - - + +
96B LEU* 4.1 10.5 - - + -
97B ILE* 1.3 74.6 - - - +
99B GLY* 1.3 59.8 + - - +
135B ASN* 5.0 0.4 - - - +
136B VAL* 3.0 14.6 - - - -
164B TYR* 4.0 21.8 - + - -
165B TRP* 3.3 5.6 - - - +
166B GLY* 2.6 50.5 + - - +
167B ILE* 3.2 25.4 - - - -
168B ILE 4.3 0.2 - - - -
94C LEU* 4.1 38.4 - - + -
139C THR* 3.6 29.4 - - - +
141C GLU* 4.6 11.4 - - + +
175C PHE* 4.6 0.7 - - - -
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Residues in contact with GLY 99 (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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98B TYR* 1.3 78.1 - - - +
100B GLN* 1.3 66.3 + - - +
135B ASN* 3.2 12.5 + - - +
136B VAL* 2.7 27.7 + - - -
164B TYR* 3.1 30.3 - - - -
165B TRP* 3.7 5.6 - - - -
139C THR 4.4 1.0 + - - -
140C TYR* 5.2 0.6 - - - -
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Residues in contact with GLN 100 (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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99B GLY* 1.3 77.9 - - - +
101B VAL* 1.3 64.3 + - - +
102B ALA* 5.3 1.2 - - - +
133B ILE* 5.2 10.3 - - + +
134B GLN 3.4 12.6 - - - +
135B ASN* 4.9 1.3 - - - +
136B VAL* 3.3 6.6 - - - +
162B ASN* 2.9 31.7 - - - +
163B THR* 3.1 5.7 - - - +
164B TYR* 2.7 61.8 + - + +
119C LYS* 5.2 15.8 - - - +
122C ASP* 5.7 1.2 - - - +
124C ILE* 4.9 13.5 - - - +
140C TYR* 4.7 14.5 - - + +
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Residues in contact with VAL 101 (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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100B GLN* 1.3 75.9 - - - +
102B ALA* 1.3 58.1 + - - +
103B PRO* 2.8 22.4 - - + +
113B PHE* 4.7 4.3 - - + -
115B VAL* 3.7 34.5 - - + -
127B LEU* 4.5 6.3 - - + -
133B ILE* 3.4 3.8 - - - +
134B GLN* 3.2 34.4 + - + +
136B VAL* 3.7 19.7 - - + -
150B LEU* 4.2 10.8 - - + -
159B LEU* 3.1 34.5 - - + -
163B THR* 3.6 2.9 - - + -
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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