Contacts of the strand formed by residues 120 - 128 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LEU* 3.9 21.8 - - + -
90A TYR* 3.5 9.2 - - + +
92A VAL* 3.8 28.9 - - + -
113A PHE* 3.9 25.6 - - + -
114A LEU* 4.0 14.3 - - + +
117A ASN* 3.5 22.9 + - + +
118A THR* 3.2 2.6 - - - +
119A HIS* 1.3 103.5 - - + +
121A ARG* 1.3 70.4 + - - +
122A LEU* 5.5 1.3 - - + -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 5.3 5.6 - - + +
89A ILE* 3.5 46.0 - - + +
90A TYR 2.9 12.4 + - - +
91A ARG* 3.4 12.2 - - + +
92A VAL 2.9 25.6 + - - +
114A LEU* 5.3 0.2 - - - -
118A THR 3.3 24.1 + - - -
119A HIS* 4.8 0.6 - - - +
120A VAL* 1.3 78.2 - - - +
122A LEU* 1.3 61.1 + - - +
147A GLY 5.7 5.2 - - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 5.7 0.2 - - + -
91A ARG* 5.9 0.2 - - - -
92A VAL* 3.3 36.1 - - + +
94A TRP* 3.8 31.6 - - + +
110A VAL* 3.8 25.6 - - + -
113A PHE* 6.2 1.8 - - + -
114A LEU* 4.0 20.3 - - + +
120A VAL* 4.3 2.0 + - + -
121A ARG* 1.3 73.7 - - - +
123A ARG* 1.3 64.7 + - - +
124A ILE* 3.8 27.6 - - + -
147A GLY 4.4 2.5 + - - +
148A ALA* 3.2 16.9 - - + +
149A GLN* 3.0 20.8 + - - +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 4.4 2.6 + - - -
91A ARG* 3.6 47.4 - - + +
92A VAL 2.9 10.2 + - - +
93A THR* 2.7 38.6 + - + +
94A TRP 2.9 25.3 + - - +
95A PHE* 5.8 1.4 - - - -
122A LEU* 1.3 75.2 - - - +
124A ILE* 1.3 62.4 + - - +
125A PHE* 3.8 23.7 - - + -
149A GLN* 3.4 37.3 + - + +
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TRP* 3.7 37.9 - - + -
96A ILE* 3.9 24.9 - - + -
100A PRO* 4.3 10.3 - - + -
122A LEU* 3.8 22.7 - - + -
123A ARG* 1.3 75.9 - - - +
125A PHE* 1.3 65.7 + - - +
126A ALA* 4.6 3.8 - - + +
143A LEU* 3.8 34.5 - - + -
148A ALA* 5.0 3.1 - - + -
149A GLN* 2.7 15.9 + - - +
150A VAL* 3.7 8.9 - - + -
151A SER* 2.8 30.7 + - - +
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Residues in contact with PHE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.8 10.1 - - + -
94A TRP 2.9 21.1 + - - +
95A PHE* 3.4 20.4 - + + -
96A ILE* 2.9 29.6 + - - +
123A ARG* 3.8 35.0 - - + -
124A ILE* 1.3 72.7 - - - +
126A ALA* 1.3 60.3 + - - +
149A GLN* 3.8 17.3 - - - -
151A SER* 3.4 28.7 - - - -
152A ILE 4.3 8.3 - - - -
153A MET* 3.5 17.7 - - + +
157A GLU* 3.9 30.7 - - + -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 3.4 9.2 - - + -
99A SER* 4.0 25.1 - - - +
124A ILE* 4.0 4.2 - - + -
125A PHE* 1.3 72.4 - - - +
127A ALA* 1.3 64.0 + - - +
128A ARG 3.6 17.3 - - - +
140A LEU* 5.9 1.8 - - + -
150A VAL* 6.1 2.2 - - + -
151A SER 3.0 12.7 + - - +
152A ILE* 3.4 18.7 - - + +
153A MET* 2.9 18.2 + - - -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.9 17.3 - - + +
24A ASN* 3.3 14.0 - - - +
96A ILE 3.0 10.8 + - - +
97A SER* 3.6 14.1 - - - +
126A ALA* 1.3 74.1 - - - +
128A ARG* 1.3 62.9 + - + +
152A ILE* 4.6 2.6 - - - +
153A MET* 3.7 26.2 - - - +
158A PHE* 3.9 16.8 - - + -
186A LEU* 3.2 18.5 - - - +
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN 2.4 25.4 + - - -
22A PHE 4.1 1.2 - - - -
23A ASN 2.6 33.8 + - - +
24A ASN* 3.7 18.6 - - - +
25A GLY 5.3 0.4 - - - -
26A ILE 3.2 18.8 + - - -
27A GLY* 3.5 6.9 - - - +
28A ARG* 3.5 14.8 - - - +
30A LYS 4.2 0.4 + - - -
97A SER* 2.7 33.0 + - - +
98A TRP* 3.0 50.6 - - + +
99A SER 3.1 23.4 + - - -
126A ALA* 3.6 9.9 - - - +
127A ALA* 1.3 81.7 - - - +
129A ILE* 1.3 63.7 + - - +
152A ILE* 5.2 0.2 - - - -
186A LEU* 3.8 7.0 - - + -
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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