Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 3B93
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLN 3.4 1.2 + - - -
92A ASN* 1.3 79.1 - - - +
94A LEU* 1.3 61.5 + - - -
95A TYR* 3.5 15.3 - - - -
141A GLU* 3.4 3.1 - - - -
142A LEU 2.7 38.0 + - - -
169A LEU* 4.0 1.3 - - - -
171A ALA 3.5 8.5 - - - -
172A ASN* 4.0 7.1 - - - +
176A ILE* 3.9 11.2 - - - +
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Residues in contact with LEU 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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93A GLY* 1.3 70.5 - - - -
95A TYR* 1.3 60.2 + - - +
139A THR* 3.5 26.0 - - + -
140A TYR 3.7 13.5 - - - +
141A GLU* 4.1 4.0 - - + +
169A LEU* 3.7 3.1 - - - +
170A LEU* 2.8 59.4 + - + -
171A ALA* 2.7 26.4 + - + +
173A PRO* 4.5 7.9 - - + -
176A ILE* 4.2 3.4 - - + +
59C MET* 4.2 10.3 - - + -
98C TYR* 3.8 35.9 - - + +
168C ILE* 4.0 23.3 - - + -
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Residues in contact with TYR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A CYS* 3.3 24.6 + - + +
79A VAL* 4.3 16.2 - - + -
89A ILE* 4.1 7.2 - - + -
91A GLN* 2.6 39.1 + - - +
93A GLY* 3.5 25.4 - - - -
94A LEU* 1.3 74.3 - - - +
96A LEU* 1.3 61.5 + - - +
97A ILE* 4.1 1.3 + - + -
138A GLY 4.0 0.3 - - - +
139A THR* 3.3 6.2 - - - +
140A TYR* 2.8 34.6 + - - +
142A LEU* 3.6 27.8 - - + -
167A ILE* 3.7 31.0 - - + -
168A ILE 3.2 14.6 - - - +
169A LEU* 3.6 26.3 - - + +
170A LEU* 4.4 0.9 - - - -
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Residues in contact with LEU 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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95A TYR* 1.3 75.1 - - - +
97A ILE* 1.3 88.6 + - - +
98A TYR* 4.2 2.8 + - + -
138A GLY* 3.5 9.4 - - - +
139A THR* 3.7 16.2 - - - +
167A ILE* 3.2 3.0 - - - -
168A ILE* 2.8 50.4 + - + +
170A LEU* 3.9 10.9 - - + +
96B LEU* 4.0 14.4 - - + -
139B THR* 3.5 24.0 - - + +
170B LEU* 3.9 22.7 - - + -
96C LEU* 3.9 18.4 - - + -
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Residues in contact with ILE 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 TYR 5.0 2.0 - - - +
96A LEU* 1.3 84.4 - - - +
98A TYR* 1.4 63.4 + - - +
117A LEU* 4.3 11.0 - - + -
124A ILE* 4.6 7.0 - - + -
136A VAL* 3.9 0.8 - - + +
137A GLY* 3.2 16.3 - - - -
138A GLY 2.6 35.3 + - - +
140A TYR* 3.8 26.2 - - + -
142A LEU* 4.7 4.9 - - + -
148A ILE* 3.9 34.1 - - + -
165A TRP* 3.8 17.9 - - + -
166A GLY 3.4 11.0 - - - +
167A ILE* 4.0 18.6 - - + -
139B THR* 5.1 0.3 + - - -
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Residues in contact with TYR 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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59A MET* 5.6 2.7 - - - -
60A ALA 4.4 1.1 + - - -
61A LYS* 4.2 2.6 - - - +
96A LEU* 4.3 4.3 - - + -
97A ILE* 1.4 77.4 - - - +
99A GLY* 1.3 64.8 + - - +
136A VAL 3.2 12.3 - - - -
164A TYR* 4.3 11.0 - + - -
165A TRP* 3.3 7.0 - - - +
166A GLY* 2.8 61.3 + - - +
167A ILE* 3.5 10.3 - - - -
94B LEU* 3.8 36.5 - - + +
139B THR* 3.7 30.3 - - + +
140B TYR* 5.7 0.2 - - - -
141B GLU* 2.9 40.6 + - + -
173B PRO* 5.6 0.2 - - - +
175B PHE* 4.0 17.8 - - - -
176B ILE* 4.3 2.8 - - - +
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Residues in contact with GLY 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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98A TYR* 1.3 88.5 - - - +
100A GLN* 1.3 61.4 + - - +
135A ASN* 3.2 14.6 - - - +
136A VAL* 3.0 30.9 + - - -
164A TYR* 3.3 16.2 - - - -
165A TRP* 3.8 2.7 - - - -
139B THR 5.2 2.9 + - - +
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Residues in contact with GLN 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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99A GLY* 1.3 75.8 - - - +
101A VAL* 1.3 61.4 + - - +
133A ILE* 3.4 31.0 - - + +
134A GLN 3.5 6.1 - - - +
135A ASN* 5.0 6.9 + - - +
136A VAL* 4.1 0.4 - - - +
162A ASN* 2.9 42.5 + - - +
163A THR* 3.3 6.4 - - - +
164A TYR* 2.7 69.7 + - + +
119B LYS* 5.9 2.8 - - - +
140B TYR* 6.3 1.2 - - - -
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Residues in contact with VAL 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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100A GLN* 1.3 79.0 - - - +
102A ALA* 1.3 60.1 + - - +
103A PRO* 3.1 23.8 - - + +
115A VAL* 4.0 19.5 - - + -
127A LEU* 3.5 25.8 - - + -
133A ILE* 3.4 1.2 - - - -
134A GLN 2.8 31.2 + - - +
136A VAL* 3.6 24.6 - - + +
150A LEU* 4.0 19.7 - - + -
152A PHE* 5.4 0.2 - - + -
158A VAL* 4.1 21.3 - - + -
163A THR* 3.9 3.4 - - + -
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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