Contacts of the strand formed by residues 54 - 60 (chain A) in PDB entry 1SQU
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 GLY 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A GLY* 3.6 2.6 - - - -
48A ILE* 2.9 36.4 + - - +
52A ILE* 4.5 1.3 - - - +
53A GLU* 1.3 75.8 - - - +
55A SER* 1.3 62.7 + - - -
129A PHE 5.6 1.6 - - - -
150A SER* 3.1 18.2 - - - -
151A VAL* 4.1 1.1 - - - -
114B THR* 3.8 5.4 + - - +
115B PRO* 3.9 12.9 - - - +
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 4.7 7.2 - - - -
46A ILE 3.2 14.4 - - - -
47A GLY* 4.2 1.8 - - - -
48A ILE* 4.3 3.3 - - - +
54A GLY* 1.3 75.7 - - - -
56A LEU* 1.3 61.4 + - - +
57A ILE* 3.7 24.4 - - - +
128A SER* 4.0 2.4 + - - -
148A HIS 4.4 0.4 - - - -
149A LEU* 2.8 32.9 - - - +
150A SER* 2.9 27.7 + - - -
114B THR* 6.3 1.1 - - - -
115B PRO 6.1 1.3 - - - -
117B THR* 5.5 7.0 - - - -
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Residues in contact with LEU 56 (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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9A LEU* 3.8 18.8 - - + -
44A THR 3.3 5.0 - - - +
45A VAL* 3.6 0.7 - - - -
46A ILE* 2.7 43.2 + - + +
48A ILE* 5.0 4.3 - - + -
55A SER* 1.3 75.7 - - - +
57A ILE* 1.3 59.8 + - - +
58A TYR* 3.5 32.9 + - + +
96A THR* 4.9 1.6 - - + -
97A ALA* 4.0 28.3 - - + +
100A LEU* 4.2 15.3 - - + -
147A LEU* 3.2 31.6 - - + -
148A HIS 3.6 2.5 - - - +
149A LEU* 3.9 13.5 - - + -
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Residues in contact with ILE 57 (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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36A ILE* 3.8 30.7 - - + -
38A ILE* 6.3 0.2 - - + -
43A VAL* 4.3 7.4 - - + -
44A THR 3.3 6.7 - - - +
45A VAL* 4.2 16.8 - - + -
55A SER* 3.7 21.1 - - - +
56A LEU* 1.3 78.9 - - - +
58A TYR* 1.3 67.1 + - - +
59A SER* 4.7 2.5 - - - -
126A ILE* 3.6 36.1 - - + -
128A SER* 3.8 7.4 - - - +
146A ASP* 3.5 2.4 - - - +
147A LEU* 3.5 4.7 - - - -
148A HIS* 2.9 39.3 + - + +
150A SER* 5.2 0.4 - - - +
117B THR* 4.7 4.3 - - - +
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Residues in contact with TYR 58 (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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13A VAL* 5.0 3.8 - - + -
42A LEU 3.7 0.5 - - - +
43A VAL* 3.0 8.3 - - - +
44A THR* 3.0 55.9 + - + -
46A ILE* 4.6 4.7 - - + -
56A LEU* 3.5 29.1 - - + +
57A ILE* 1.3 72.9 - - - +
59A SER* 1.3 60.1 + - - +
60A PHE* 3.7 11.7 - - + -
92A LEU* 6.5 0.7 - - + -
93A GLY* 3.9 23.7 + - - -
96A THR* 2.9 40.9 - - + +
137A ILE* 5.3 5.8 - - + -
145A PHE* 4.8 16.4 - + + -
146A ASP 3.9 2.9 - - - -
147A LEU* 3.3 30.4 - - + +
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Residues in contact with SER 59 (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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36A ILE* 6.5 0.7 - - - -
38A ILE* 3.9 19.4 - - - +
39A PRO* 4.3 0.8 - - - +
40A HIS* 3.6 12.4 + - - +
42A LEU 3.5 2.5 - - - -
43A VAL* 3.7 17.8 - - - +
57A ILE* 4.7 2.5 - - - -
58A TYR* 1.3 75.3 - - - +
60A PHE* 1.3 61.3 + - - +
145A PHE* 3.3 7.3 - - - -
146A ASP* 2.8 63.7 + - - +
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Residues in contact with PHE 60 (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 HIS* 3.2 12.0 - - - +
42A LEU* 2.9 57.3 + - + +
44A THR* 3.2 28.0 - - - -
58A TYR* 3.7 13.9 - - + -
59A SER* 1.3 80.3 - - - +
61A SER* 1.3 60.1 + - - +
64A THR* 4.0 4.5 - - + -
65A ALA* 3.9 33.9 - - + -
68A VAL* 6.0 0.9 - - + -
89A ILE* 3.3 29.8 - - + -
118A VAL* 4.6 2.7 - - + -
144A ASP 3.7 11.0 - - - +
145A PHE* 3.3 34.1 - + + -
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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