Contacts of the strand formed by residues 97 - 103 (chain F) in PDB entry 3CB4
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 97 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F ASN 3.5 4.4 + - - -
7F PHE* 3.2 24.1 - - - -
8F SER 3.5 0.5 + - - -
95F CYS* 3.4 10.6 - - - +
96F GLU* 1.3 81.7 - - - +
98F ALA* 1.3 63.5 + - - +
124F LEU* 3.7 7.4 - - - +
125F GLU 3.0 17.3 - - - -
180F ILE* 3.8 12.9 - - - +
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 4.3 1.3 - - - -
8F SER* 3.3 23.6 - - - +
10F ILE* 4.5 17.5 - - + -
92F LEU* 4.7 7.2 - - + -
97F GLY* 1.3 75.7 - - - +
99F LEU* 1.3 62.8 + - - +
119F ALA* 4.9 3.6 - - + -
124F LEU* 4.8 4.3 - - + -
125F GLU 2.6 11.2 + - - +
126F VAL* 3.3 10.0 - - + -
127F VAL* 2.7 34.3 + - - +
180F ILE* 4.0 3.6 - - - +
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.6 31.2 - - + -
8F SER 2.9 9.3 + - - +
9F ILE* 3.8 16.8 - - + +
10F ILE* 2.9 31.2 + - - +
20F LEU* 4.0 21.3 - - + -
24F ILE* 4.3 3.8 - - + -
98F ALA* 1.3 74.8 - - - +
100F LEU* 1.3 59.6 + - - +
101F VAL* 3.7 5.3 + - + -
126F VAL* 5.0 0.7 - - - -
127F VAL* 3.5 30.5 - - + +
129F VAL* 4.4 10.3 - - + -
172F VAL* 4.2 12.6 - - + -
176F LEU* 4.1 24.5 - - + -
180F ILE* 5.0 1.3 - - + -
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ILE* 3.6 28.9 - - + +
98F ALA 4.1 0.2 + - - -
99F LEU* 1.3 71.6 - - - +
101F VAL* 1.3 61.4 + - - +
102F VAL* 3.3 24.3 + - + +
108F VAL* 5.0 3.4 - - + -
112F THR* 4.0 13.2 - - - +
113F LEU* 6.4 0.2 - - + -
116F CYS* 3.7 29.6 - - - -
126F VAL* 4.1 14.1 - - + -
127F VAL 2.8 14.0 + - - +
128F PRO* 4.1 4.2 - - + +
129F VAL* 3.1 24.2 + - - +
147F ILE* 4.4 13.9 - - + -
151F VAL* 4.3 20.9 - - + -
153F ILE* 5.3 3.4 - - + -
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Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ILE* 3.7 25.8 - - + -
10F ILE 3.1 11.5 + - - +
11F ALA* 3.9 22.3 - - + +
12F HIS 4.7 1.9 + - - -
20F LEU* 3.5 40.2 - - + +
99F LEU* 4.5 7.9 - - + -
100F LEU* 1.3 68.8 - - - +
102F VAL* 1.3 61.7 + - - +
103F ASP 4.3 0.5 + - - -
112F THR* 5.9 0.9 - - - +
129F VAL* 3.6 8.5 - - + +
131F ASN* 3.7 35.0 - - + +
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Residues in contact with VAL 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LEU* 3.6 29.2 - - + +
101F VAL* 1.3 79.2 - - - +
103F ASP* 1.3 71.0 + - - +
104F ALA* 3.4 0.7 + - - -
107F GLY 3.8 2.9 - - - +
108F VAL* 3.8 31.2 - - + +
129F VAL 2.8 14.2 + - - +
130F LEU* 3.4 3.9 - - + +
131F ASN* 2.7 32.8 + - - -
143F VAL* 3.7 17.7 - - + -
147F ILE* 3.8 25.8 - - + -
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Residues in contact with ASP 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ILE* 3.9 17.8 - - + +
101F VAL* 4.3 0.8 + - - +
102F VAL* 1.3 78.7 - - - +
104F ALA* 1.3 62.3 + - - +
105F GLY* 3.1 21.7 + - - -
106F GLN* 3.8 26.9 - - + +
107F GLY 3.1 23.1 + - - +
109F GLU* 6.0 0.7 - - - +
131F ASN* 3.8 7.6 - - - +
132F LYS* 3.4 40.4 - - - +
135F LEU* 4.5 6.9 - - - +
143F VAL* 3.8 2.6 - - - +
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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