Contacts of the strand formed by residues 126 - 136 (chain B) in PDB entry 5F0P
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 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ILE* 4.1 5.8 - - + -
77B GLU 3.3 3.8 - - - +
78B LEU* 3.7 20.4 - - + -
121B TYR* 3.9 9.1 - - + -
123B GLY* 2.8 28.4 + - - -
124B ALA 3.5 1.4 - - - +
125B ASN* 1.3 85.9 - - - +
127B ARG* 1.3 70.1 + - - +
215B GLU* 4.0 8.2 + - - +
217B THR* 3.3 23.8 - - + +
268B PHE* 3.6 52.5 - - + -
407B EDO 3.6 1.1 - - - -
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Residues in contact with ARG 127 (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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31B THR* 5.4 5.0 - - - +
32B GLU* 3.8 27.1 + - - +
75B GLN 3.9 0.7 - - - +
76B ILE* 3.3 4.0 - - - +
77B GLU* 2.7 65.3 + - - +
80B ASN* 4.9 4.8 + - - -
121B TYR 3.3 6.5 - - - +
122B ILE* 4.3 38.6 - - + +
123B GLY 4.7 1.8 + - - +
126B VAL* 1.3 78.6 - - - +
128B LEU* 1.3 61.0 + - - +
129B ARG* 4.1 10.9 - - + +
407B EDO 3.5 27.9 + - - +
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Residues in contact with LEU 128 (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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29B MSE 4.7 1.4 - - - +
75B GLN 3.4 2.7 - - - -
76B ILE* 3.6 28.5 - - + +
88B PHE* 3.7 22.7 - - + -
118B TYR* 3.5 26.0 - - + -
119B GLU 3.8 15.9 - - - +
120B SER* 3.4 6.6 - - - -
121B TYR* 2.8 41.9 + - + +
122B ILE* 5.3 0.2 - - - +
126B VAL* 4.7 0.2 - - - +
127B ARG* 1.3 72.8 - - - +
129B ARG* 1.3 63.2 + - - +
130B TYR* 3.8 17.5 - - + -
264B VAL* 3.6 17.5 - - + -
268B PHE* 4.0 14.6 - - + -
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Residues in contact with ARG 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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29B MSE 5.8 4.3 - - + -
73B VAL 4.0 0.5 - - - +
74B GLY* 3.6 0.5 - - - -
75B GLN* 3.0 40.0 + - + +
77B GLU* 3.0 38.5 + - - +
120B SER* 4.9 3.6 - - - -
122B ILE* 6.2 4.5 - - + -
127B ARG* 5.1 12.1 - - + +
128B LEU* 1.3 76.7 - - - +
130B TYR* 1.3 67.1 + - - +
131B PHE* 3.3 31.6 - - + +
146B GLU* 2.9 28.3 + - - +
148B ASP* 3.0 35.4 + - - +
149B LEU 5.4 1.3 - - - +
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Residues in contact with TYR 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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72B PHE* 3.6 28.5 - + + -
73B VAL 3.1 5.2 - - - +
74B GLY* 3.6 11.4 - - - -
88B PHE* 3.4 25.7 - + - -
89B VAL* 5.2 0.9 - - + -
115B GLU 4.9 0.7 - - - -
116B LYS* 3.3 29.6 - - + -
118B TYR 2.7 43.8 + - - -
120B SER* 3.7 12.1 - - - -
128B LEU* 3.8 13.5 - - + -
129B ARG* 1.3 77.1 - - - +
131B PHE* 1.3 65.3 + - - +
148B ASP* 3.7 7.4 - - - +
149B LEU* 3.1 37.8 + - + +
151B VAL* 3.5 24.7 - - + -
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Residues in contact with PHE 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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71B GLU 3.8 0.2 - - - +
72B PHE* 3.7 2.0 - - - -
73B VAL* 2.8 67.3 + - + +
75B GLN* 3.5 29.6 - - + -
129B ARG* 3.3 39.5 - - - +
130B TYR* 1.3 80.3 - - - +
132B LEU* 1.3 70.7 + - - +
133B LYS* 4.0 18.8 - - + -
146B GLU* 3.5 25.8 - - + -
147B TYR 3.3 18.8 - - - +
148B ASP* 3.8 9.6 - - - +
149B LEU* 4.4 6.7 - - - +
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Residues in contact with LEU 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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16B ILE* 3.8 38.6 - - + -
18B LEU* 4.2 6.1 - - + -
48B VAL* 4.1 17.9 - - + -
70B ILE* 4.5 4.9 - - + -
71B GLU 3.2 13.0 - - - +
72B PHE* 3.9 22.9 - - + -
109B PHE* 3.9 15.3 - - + -
111B PHE* 4.0 21.1 - - + -
131B PHE* 1.3 74.4 - - - +
133B LYS* 1.3 59.5 + - - +
134B VAL 4.2 0.7 - - - -
145B LYS 3.7 1.1 - - - +
146B GLU* 3.3 2.9 - - - -
147B TYR* 2.7 48.7 + - + +
149B LEU* 4.3 9.6 - - + -
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Residues in contact with LYS 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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69B ARG* 5.2 0.4 - - - +
70B ILE* 3.5 1.4 - - - -
71B GLU* 2.8 68.6 + - + +
73B VAL* 4.6 2.7 - - + -
75B GLN* 5.8 0.4 + - - -
87B GLU* 4.4 15.0 + - - -
131B PHE* 4.0 22.5 + - + -
132B LEU* 1.3 73.6 - - - +
134B VAL* 1.3 63.7 + - - +
135B THR* 4.0 9.2 + - - +
144B VAL* 3.9 27.1 - - + -
145B LYS 3.4 3.6 - - - +
146B GLU* 3.8 21.6 + - + +
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Residues in contact with VAL 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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14B ILE* 3.7 30.9 - - + +
16B ILE* 3.6 25.6 - - + -
52B VAL* 3.8 23.8 - - + -
54B LEU* 5.2 0.4 - - + -
68B ILE* 4.4 9.9 - - + -
69B ARG 3.5 11.4 - - - +
70B ILE* 3.7 24.2 - - + -
95B LEU* 5.1 0.2 - - + -
133B LYS* 1.3 72.7 - - - +
135B THR* 1.3 68.4 + - - +
136B ILE* 4.8 0.9 - - + +
143B LEU 3.9 0.6 - - - +
144B VAL* 3.4 5.0 - - - +
145B LYS 2.9 35.1 + - - +
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Residues in contact with THR 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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67B GLY 4.0 0.3 - - - +
68B ILE* 3.4 3.3 - - - +
69B ARG* 3.0 61.1 + - - +
71B GLU* 4.3 3.5 + - - -
133B LYS* 4.0 15.5 + - - +
134B VAL* 1.3 76.6 + - - +
136B ILE* 1.3 65.3 + - - +
137B VAL* 3.9 11.3 + - + +
142B ASP* 3.5 34.8 - - + +
143B LEU 3.5 3.4 - - - +
144B VAL* 4.4 8.4 - - + +
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Residues in contact with ILE 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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12B CYS* 4.5 6.7 - - - -
14B ILE* 3.9 29.2 - - + -
54B LEU* 3.9 26.0 - - + -
63B LEU* 4.7 8.7 - - + -
65B HIS* 3.7 26.9 - - + -
67B GLY 3.7 2.7 - - - -
68B ILE* 3.9 27.1 - - + -
134B VAL* 4.3 0.9 - - + -
135B THR* 1.3 73.9 - - - +
137B VAL* 1.3 64.1 + - - +
138B ARG* 3.6 9.0 + - + +
142B ASP* 3.6 3.1 - - - +
143B LEU* 2.9 51.5 + - + +
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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