Contacts of the strand formed by residues 125 - 131 (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 GLU 125 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96F GLU 3.1 9.6 + - - +
97F GLY* 3.0 3.3 - - - -
98F ALA 2.6 33.1 + - - +
123F ASP 4.2 0.6 + - - -
124F LEU* 1.3 69.6 - - - +
126F VAL* 1.3 58.8 + - - +
127F VAL* 3.8 3.8 + - + +
179F ASP* 3.4 40.2 - - - +
180F ILE* 4.0 17.0 - - + +
181F PRO* 3.9 11.7 - - + -
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Residues in contact with VAL 126 (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* 5.4 2.9 - - + -
98F ALA* 3.3 15.7 - - + +
99F LEU 5.0 0.2 - - - -
100F LEU* 4.1 24.2 - - + -
116F CYS* 4.2 16.6 - - - -
119F ALA* 4.5 14.8 - - + -
120F MET* 4.0 25.1 - - + +
124F LEU* 3.4 16.5 + - + +
125F GLU* 1.3 74.2 + - - +
127F VAL* 1.3 61.7 + - - +
128F PRO* 3.4 11.4 - - - +
153F ILE* 4.3 26.4 - - + +
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Residues in contact with VAL 127 (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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98F ALA 2.7 13.8 + - - +
99F LEU* 3.5 25.7 - - + -
100F LEU* 2.8 29.6 + - - -
125F GLU* 4.6 4.3 - - + +
126F VAL* 1.3 72.1 - - - +
128F PRO* 1.3 79.1 - - + +
129F VAL* 3.6 6.8 + - + +
159F VAL* 5.3 0.9 - - + -
172F VAL* 5.4 1.6 - - + +
175F ARG* 3.8 27.1 - - + -
176F LEU* 4.7 9.2 - - - +
179F ASP* 4.7 14.6 - - + +
180F ILE* 4.3 21.8 - - + -
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Residues in contact with PRO 128 (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* 4.1 9.4 - - + +
126F VAL 3.4 9.6 - - - +
127F VAL* 1.3 91.9 - - + +
129F VAL* 1.3 64.1 + - - +
130F LEU 4.3 0.2 - - - -
147F ILE* 4.7 9.9 - - + -
153F ILE* 4.4 12.3 - - + -
154F ASP 3.4 25.4 - - - +
155F ALA* 3.8 23.6 - - + -
157F ASP 5.7 0.7 - - - -
158F ALA* 4.2 11.7 - - + -
159F VAL* 3.8 16.3 + - - +
175F ARG* 6.4 0.4 - - - +
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Residues in contact with VAL 129 (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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20F LEU* 4.2 12.6 - - + -
99F LEU* 4.4 13.7 - - + -
100F LEU 3.1 11.3 + - - +
101F VAL* 4.2 9.2 - - + -
102F VAL* 2.8 32.4 + - - +
127F VAL* 3.9 17.5 - - + +
128F PRO* 1.3 79.7 - - - +
130F LEU* 1.3 65.3 + - - +
131F ASN 4.7 0.9 - - - +
147F ILE* 5.6 0.8 - - - +
159F VAL* 3.5 7.9 - - + +
161F CYS* 4.0 15.5 - - - -
172F VAL* 3.8 42.8 - - + -
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Residues in contact with LEU 130 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102F VAL 3.4 3.8 - - - +
104F ALA* 4.8 5.4 - - + -
128F PRO 4.3 0.2 - - - -
129F VAL* 1.3 72.2 - - - +
131F ASN* 1.3 60.7 + - - +
133F ILE* 4.4 6.0 - - + +
140F PRO* 4.0 20.9 - - + +
143F VAL* 3.8 30.7 - - + -
144F ALA* 4.5 9.9 - - + +
147F ILE* 3.8 20.4 - - + -
158F ALA* 4.0 22.9 - - + -
159F VAL 2.9 9.4 + - - +
160F ARG* 3.1 41.4 - - + +
161F CYS* 3.0 27.7 + - - +
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Residues in contact with ASN 131 (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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19F THR* 5.5 0.9 - - - -
20F LEU* 4.5 3.6 + - - +
23F ARG* 2.6 44.9 + - - +
101F VAL* 3.7 30.6 - - + +
102F VAL 2.7 16.5 + - - +
103F ASP* 4.6 1.8 - - - +
104F ALA* 3.0 26.7 + - - +
129F VAL* 3.6 1.0 + - + +
130F LEU* 1.3 72.7 - - - +
132F LYS* 1.3 94.1 + - + +
133F ILE 3.4 3.2 + - - -
161F CYS* 3.2 17.2 + - - -
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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