Contacts of the strand formed by residues 120 - 128 (chain B) in PDB entry 5SWW
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 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 3.9 21.8 - - + -
90B TYR* 3.4 10.8 - - + +
92B VAL* 3.7 29.8 - - + -
113B PHE* 4.1 24.9 - - + -
114B LEU* 4.0 14.4 - - + +
117B ASN* 3.5 20.5 + - + +
118B THR* 3.2 3.7 - - - +
119B HIS* 1.3 106.5 - - + +
121B ARG* 1.3 69.8 + - - +
122B LEU* 5.0 1.1 - - + +
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Residues in contact with ARG 121 (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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40B LEU* 5.3 5.1 - - + +
89B ILE* 3.3 48.0 - - - +
90B TYR 2.9 9.8 + - - +
91B ARG* 3.4 12.3 - - + +
92B VAL 2.9 25.1 + - - +
114B LEU* 5.1 0.4 - - - -
118B THR* 3.7 23.6 + - - -
119B HIS* 5.2 0.4 - - - +
120B VAL* 1.3 76.5 - - - +
122B LEU* 1.3 59.8 + - - +
147B GLY 5.2 9.0 - - - +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 5.7 0.2 - - + -
91B ARG* 6.0 0.2 - - - -
92B VAL* 3.3 37.7 - - + +
94B TRP* 3.7 32.5 - - + +
110B VAL* 3.8 24.5 - - + -
113B PHE* 6.1 2.5 - - + -
114B LEU* 3.9 23.7 - - + +
120B VAL* 4.2 2.1 + - + -
121B ARG* 1.3 74.5 - - - +
123B ARG* 1.3 64.9 + - - +
124B ILE* 3.8 27.6 - - + -
147B GLY 4.4 2.4 + - - +
148B ALA* 3.1 13.5 - - + +
149B GLN* 2.9 21.7 + - - +
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Residues in contact with ARG 123 (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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38B GLU* 4.1 1.2 + - - -
91B ARG* 3.5 46.3 - - + +
92B VAL 2.9 9.7 + - - +
93B THR* 2.6 34.3 + - + +
94B TRP 2.9 25.8 + - - +
122B LEU* 1.3 75.0 - - - +
124B ILE* 1.3 61.8 + - - +
125B PHE* 3.8 19.7 - - + -
149B GLN* 3.4 40.0 + - + +
203B GOL 3.2 37.3 + - - -
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Residues in contact with ILE 124 (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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94B TRP* 3.6 38.1 - - + -
96B ILE* 3.8 26.0 - - + -
100B PRO* 4.2 10.3 - - + -
122B LEU* 3.8 22.2 - - + -
123B ARG* 1.3 76.7 - - - +
125B PHE* 1.3 65.4 + - - +
126B ALA* 4.6 3.4 - - + +
143B LEU* 3.7 35.0 - - + -
148B ALA* 5.1 2.9 - - + -
149B GLN* 2.8 14.7 + - - +
150B VAL* 3.8 7.3 - - + +
151B SER* 2.9 30.3 + - - +
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Residues in contact with PHE 125 (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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93B THR* 3.8 19.7 - - + -
94B TRP 2.9 21.3 + - - +
95B PHE* 3.5 21.3 - + + -
96B ILE* 2.9 29.8 + - - +
123B ARG* 3.8 24.7 - - + -
124B ILE* 1.3 73.4 - - - +
126B ALA* 1.3 60.0 + - - +
149B GLN* 3.8 17.3 - - - -
151B SER* 3.3 28.3 - - - -
152B ILE 4.2 8.7 - - - -
153B MET* 3.5 18.1 - - + +
157B GLU* 3.9 31.2 - - + -
203B GOL 4.8 3.6 - - - -
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Residues in contact with ALA 126 (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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96B ILE* 3.4 10.5 - - + -
99B SER* 4.0 25.4 - - - +
124B ILE* 4.0 4.2 - - + -
125B PHE* 1.3 73.4 - - - +
127B ALA* 1.3 64.1 + - - +
128B ARG 3.6 16.8 - - - +
140B LEU* 5.9 1.8 - - + -
150B VAL* 6.3 1.6 - - + -
151B SER 2.9 12.5 + - - +
152B ILE* 3.3 18.9 - - + +
153B MET* 2.9 18.9 + - - -
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Residues in contact with ALA 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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22B PHE* 3.9 27.6 - - + +
24B ASN* 3.3 13.8 + - + +
96B ILE 3.0 10.7 + - - +
97B SER* 3.6 14.8 - - - +
126B ALA* 1.3 74.4 - - - +
128B ARG* 1.3 62.4 + - + +
152B ILE* 4.6 3.2 - - - +
153B MET* 3.7 26.3 - - - +
158B PHE* 3.9 6.4 - - + -
186B LEU* 3.2 18.6 - - - +
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Residues in contact with ARG 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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21B ASN* 2.4 26.0 + - - +
22B PHE* 4.1 1.2 - - - +
23B ASN 2.6 32.6 + - - -
24B ASN* 3.7 18.6 - - - +
25B GLY 5.2 0.9 - - - -
26B ILE 3.2 19.3 + - - -
27B GLY* 3.5 8.0 - - - -
28B ARG* 3.5 12.7 - - - +
30B LYS 4.2 0.8 + - - -
97B SER* 2.6 32.6 + - - +
98B TRP* 3.0 51.7 - - + +
99B SER 3.1 23.0 + - - -
126B ALA* 3.6 9.7 - - - +
127B ALA* 1.3 80.4 - - - +
129B ILE* 1.3 64.5 + - - +
152B ILE* 5.2 0.7 - - - -
186B LEU* 3.8 8.3 - - + -
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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