Contacts of the strand formed by residues 113 - 120 (chain B) in PDB entry 3FBK
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 ARG 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A GLU* 5.8 2.5 - - - +
158A HIS* 4.6 11.7 - - - -
74B LEU* 3.3 4.4 - - - -
75B ILE* 2.8 46.0 + - + +
111B GLN 5.0 3.1 - - - +
112B LYS* 1.3 80.7 - - - +
114B LEU* 1.3 62.9 + - - +
115B LEU 3.4 1.3 + - - -
135B SER* 2.9 42.6 + - - -
136B PHE 3.4 5.8 - - - +
137B GLY* 3.6 11.6 - - - +
138B VAL* 4.1 3.4 - - - -
161B ARG 3.2 17.1 + - - -
162B THR* 3.3 20.7 + - - +
163B LYS* 3.4 2.2 - - - +
201B SO4 2.9 41.8 + - - -
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Residues in contact with LEU 114 (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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41B ILE* 3.7 22.0 - - + -
48B LEU* 4.1 17.0 - - + -
50B LEU* 3.6 25.8 - - + -
72B ILE* 3.7 27.6 - - + -
73B SER 3.6 4.0 - - - +
74B LEU* 3.6 22.2 - - + -
103B PHE* 4.6 6.7 - - + -
113B ARG* 1.3 71.2 - - - +
115B LEU* 1.3 58.5 + - - +
116B VAL* 4.0 4.1 + - + -
135B SER* 3.1 5.6 - - - -
136B PHE* 2.7 45.0 + - + +
138B VAL* 4.1 4.0 - - + +
141B LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS 3.6 1.4 - - - +
72B ILE* 3.4 6.2 - - - +
73B SER* 2.8 47.7 + - - +
75B ILE* 3.9 36.1 - - + -
113B ARG 3.4 1.4 + - - -
114B LEU* 1.3 71.5 - - - +
116B VAL* 1.3 60.5 + - - +
117B THR* 3.5 22.2 - - - +
133B CYS* 4.2 8.3 - - + -
134B MSE 3.6 14.6 - - - +
135B SER* 4.2 2.0 - - - -
160B GLY 4.0 13.7 - - - +
161B ARG* 3.6 33.9 - - + +
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Residues in contact with VAL 116 (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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37B LEU* 3.7 21.5 - - + -
39B LEU* 4.3 11.4 - - + -
41B ILE* 5.2 0.7 - - + -
50B LEU* 4.8 11.7 - - + -
52B ILE* 5.3 3.1 - - + -
70B VAL* 3.7 24.2 - - + -
71B LYS 3.7 3.4 - - - +
72B ILE* 4.6 12.6 - - + -
114B LEU* 4.7 4.7 - - + +
115B LEU* 1.3 77.2 - - - +
117B THR* 1.3 63.1 + - - +
118B VAL* 4.4 0.6 + - + -
133B CYS* 3.2 4.7 - - - +
134B MSE 2.9 41.9 + - + +
136B PHE* 4.3 23.8 - - + -
154B LEU* 5.4 1.4 - - + +
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Residues in contact with THR 117 (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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69B TYR 3.8 0.5 - - - +
70B VAL* 3.3 3.5 - - - -
71B LYS* 2.8 42.6 + - - -
115B LEU* 3.5 25.3 - - - +
116B VAL* 1.3 74.8 - - - +
118B VAL* 1.3 74.1 + - - +
119B TRP* 3.2 37.0 - - + +
130B LEU* 3.9 18.7 - - + +
132B GLY 3.6 8.7 - - - +
133B CYS* 3.5 6.4 - - + +
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Residues in contact with VAL 118 (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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37B LEU* 4.4 13.2 - - + -
58B LEU* 4.4 9.6 - - + -
68B PRO* 3.9 14.4 - - + -
69B TYR 3.4 9.6 - - - +
70B VAL* 4.2 17.0 - - + -
97B PHE* 5.6 1.6 - - + -
116B VAL* 5.7 0.2 - - + -
117B THR* 1.3 79.9 - - - +
119B TRP* 1.3 62.6 + - - +
130B LEU 3.9 0.2 - - - -
131B ILE* 2.9 52.3 + - + -
132B GLY 2.9 13.7 + - - +
154B LEU* 3.6 31.9 - - + -
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Residues in contact with TRP 119 (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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76A PRO* 4.1 11.9 - - + -
77A GLU 3.6 17.5 - - - -
78A ASP* 3.5 41.3 - - + -
67B ASP 3.7 0.5 - - - +
68B PRO* 3.1 25.3 - - - +
69B TYR* 2.9 49.8 + + + +
71B LYS* 3.9 19.7 - - + +
117B THR* 3.2 40.1 - - + +
118B VAL* 1.3 72.8 - - - +
120B ASN* 1.3 61.3 + - - +
121B ARG 3.7 0.6 + - - -
128B SER* 3.7 21.8 - - - -
129B GLY 3.4 21.8 - - - -
130B LEU* 3.8 18.2 - - + -
131B ILE* 3.9 4.0 - - - -
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Residues in contact with ASN 120 (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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60B SER* 3.7 24.2 + - - -
62B GLN* 3.2 33.2 + - - +
65B THR 3.7 14.1 + - - +
66B CYS* 3.4 6.8 - - - -
67B ASP* 2.8 33.1 + - - +
119B TRP* 1.3 70.0 - - - +
121B ARG* 1.3 68.0 + - - +
122B ALA* 4.7 0.2 - - - +
128B SER* 3.2 5.2 - - - -
129B GLY 2.8 31.9 + - - +
131B ILE* 3.8 15.9 - - + +
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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