Contacts of the strand formed by residues 128 - 136 (chain B) in PDB entry 3FA6
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 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASN* 4.4 2.2 - - + +
17B GLU* 3.9 28.9 - - + +
18B LEU* 3.7 36.0 - - + +
21B VAL* 3.4 32.5 - - + -
123B MET 3.9 0.3 - - - +
124B THR* 3.3 6.4 - - - -
125B ALA 3.0 34.7 + - - +
127B ASP* 1.3 79.8 - - + +
129B VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 129 (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 GLU* 4.0 5.0 - - - +
14B ASN* 3.1 28.3 + - - +
122B THR* 3.5 29.6 - - + -
123B MET 3.7 2.7 - - - +
124B THR* 4.3 12.1 - - + +
127B ASP 3.6 10.9 + - - +
128B VAL* 1.3 78.5 - - - +
130B CYS* 1.3 61.5 + - - +
131B THR* 4.1 9.8 + - - +
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Residues in contact with CYS 130 (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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12B SER* 5.0 0.2 - - - -
13B GLU 3.1 14.6 - - - +
14B ASN* 3.7 11.9 - - - +
15B PHE* 3.6 27.8 - - - -
18B LEU* 4.0 15.3 - - + -
121B ASP 3.7 0.5 - - - +
122B THR* 3.3 5.5 - - - +
123B MET* 2.8 61.5 + - + +
128B VAL 4.1 0.8 - - - -
129B VAL* 1.3 73.0 - - - +
131B THR* 1.3 63.3 + - - +
132B LYS* 4.1 11.7 - - - -
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Residues in contact with THR 131 (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 ARG* 4.1 0.9 - - - +
12B SER* 3.4 2.1 - - - -
13B GLU* 2.8 55.2 + - - +
120B ILE* 3.7 28.5 - - + -
121B ASP 3.4 3.6 - - - +
122B THR* 4.3 6.3 + - - +
129B VAL* 4.1 12.5 + - - +
130B CYS* 1.3 77.6 + - - +
132B LYS* 1.4 64.6 + - - +
133B VAL* 4.3 13.5 - - + +
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Residues in contact with LYS 132 (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 ILE* 3.9 19.2 - - + +
11B ARG 3.3 4.0 - - - -
12B SER* 3.9 12.8 - - - +
15B PHE* 3.5 38.2 - - - -
39B PRO* 4.4 5.5 - - - +
119B LEU 3.7 1.0 - - - +
120B ILE* 3.6 2.6 - - - +
121B ASP* 2.8 39.2 + - + +
123B MET* 3.9 7.0 - - + -
130B CYS* 4.1 6.1 - - - -
131B THR* 1.4 78.1 - - - +
133B VAL* 1.4 63.8 + - - +
134B PHE* 3.7 19.4 - - + -
138B LSR 1.3 75.6 - - + +
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Residues in contact with VAL 133 (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 ILE* 3.5 4.3 - - - +
10B ILE* 2.8 37.9 + - + -
11B ARG* 2.9 47.3 + - + +
118B GLU* 3.5 43.1 - - + +
119B LEU 3.4 4.7 - - - +
120B ILE* 4.8 11.0 - - + -
131B THR* 4.3 15.9 - - + -
132B LYS* 1.4 77.5 - - - +
134B PHE* 1.3 58.4 + - - +
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Residues in contact with PHE 134 (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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7B TRP* 3.8 32.3 - - + -
8B LYS 3.1 9.6 - - - +
9B ILE* 3.5 36.6 - - + -
10B ILE* 4.4 0.9 - - - +
39B PRO* 4.0 11.7 - - + -
41B VAL* 3.6 29.6 - - + -
118B GLU* 3.4 4.5 - - - +
119B LEU* 2.8 49.8 + - + +
121B ASP* 4.0 16.4 - - + -
132B LYS* 3.7 36.6 - - + -
133B VAL* 1.3 75.4 - - - +
135B VAL* 1.3 69.5 + - - +
138B LSR 5.4 2.7 - - + -
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Residues in contact with VAL 135 (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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7B TRP* 3.3 10.9 - - - -
8B LYS* 2.9 54.8 + - + +
10B ILE* 3.7 33.7 - - + -
116B ASP 5.9 0.2 - - - +
117B GLY 4.2 5.8 - - - +
118B GLU* 4.1 14.6 - - + +
134B PHE* 1.3 80.3 - - - +
136B ARG* 1.3 68.5 + - - +
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Residues in contact with ARG 136 (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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2B ASN 3.0 27.7 + - - -
4B SER 3.0 22.3 + - - -
5B GLY* 3.9 8.0 - - - -
6B ASN 3.5 7.2 - - - +
7B TRP* 3.4 39.3 - - + -
8B LYS* 4.4 1.8 - - - +
113B LEU* 4.5 5.5 - - - +
117B GLY* 4.4 12.6 + - - +
135B VAL* 1.3 83.2 - - - +
137B GLU* 1.3 69.0 + - - +
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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