Contacts of the strand formed by residues 139 - 149 (chain A) in PDB entry 7KHI
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 SER 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ASP* 5.7 0.7 - - - +
71A LYS* 3.6 18.6 + - - +
104A LYS 3.4 5.8 - - - -
105A SER* 3.0 27.9 - - - +
137A ASN* 3.2 13.3 + - - -
138A ALA* 1.3 74.0 - - - +
140A ILE* 1.3 63.6 + - - +
141A SER 4.3 0.5 + - - -
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Residues in contact with ILE 140 (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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61A ILE* 5.5 6.1 - - + -
71A LYS* 4.2 23.3 - - + +
72A GLU 5.8 0.2 - - - +
74A VAL* 4.1 22.4 - - + -
102A LEU* 3.7 4.0 - - + +
103A ASN* 3.4 2.8 - - - +
104A LYS* 2.9 39.7 + - + +
110A VAL* 4.0 29.8 - - + -
131A CYS* 4.4 15.3 - - + -
133A LEU* 4.2 15.0 - - + -
139A SER* 1.3 78.4 - - - +
141A SER* 1.3 61.7 + - - +
142A MET* 4.7 16.8 - - + -
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Residues in contact with SER 141 (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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61A ILE* 3.5 16.1 - - - +
62A ASP* 3.3 31.9 + - - +
102A LEU 3.3 1.1 - - - -
103A ASN* 2.8 26.2 - - - -
139A SER 4.3 0.6 + - - -
140A ILE* 1.3 73.6 - - - +
142A MET* 1.3 64.9 + - - +
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Residues in contact with MET 142 (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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59A VAL* 4.3 10.1 - - + -
60A GLU 3.1 15.3 - - - +
61A ILE* 3.5 30.3 - - + -
81A ILE* 4.7 7.4 - - + -
85A LEU* 4.5 11.7 - - + -
101A THR* 3.4 5.4 - - - -
102A LEU* 2.9 70.2 + - + +
103A ASN* 3.6 1.5 + - - +
130A ILE* 4.1 20.0 - - + -
131A CYS* 5.2 0.4 - - - -
140A ILE* 4.7 17.9 - - + -
141A SER* 1.3 78.2 - - - +
143A ARG* 1.3 66.7 + - - +
144A ILE* 4.6 9.2 - - + -
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Residues in contact with ARG 143 (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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58A GLU* 4.7 0.7 - - - +
59A VAL* 3.5 2.3 - - - -
60A GLU* 2.9 75.4 + - + +
62A ASP* 5.9 6.1 - - - +
99A ILE* 4.0 19.5 - - + -
100A LEU 3.2 8.5 - - - +
101A THR* 4.6 12.6 - - + -
142A MET* 1.3 79.4 - - - +
144A ILE* 1.3 62.9 + - - +
145A LYS* 3.9 1.4 + - - +
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Residues in contact with ILE 144 (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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56A VAL* 3.3 45.5 - - + -
58A GLU 3.6 3.8 - - - +
59A VAL* 4.1 17.0 - - + +
85A LEU* 4.1 22.7 - - + -
88A LEU* 4.9 5.4 - - + -
98A VAL 3.6 2.1 - - - +
99A ILE* 3.5 2.1 - - - -
100A LEU* 2.8 49.0 + - + +
102A LEU* 4.8 7.9 - - + -
115A ILE* 4.0 26.5 - - + -
142A MET* 4.6 15.3 - - + -
143A ARG* 1.3 74.3 - - - +
145A LYS* 1.3 60.1 + - - +
146A VAL* 3.8 2.7 + - + +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A VAL* 4.0 0.5 - - - -
57A THR* 3.0 26.5 + - - +
58A GLU* 2.8 60.4 + - + +
97A GLU* 4.8 12.3 - - + +
98A VAL 3.3 10.1 - - - +
99A ILE* 4.0 22.2 - - + +
143A ARG 3.9 2.3 + - - +
144A ILE* 1.3 71.3 - - - +
146A VAL* 1.3 62.1 + - - +
147A GLN* 2.6 38.2 + - - +
170A ARG* 5.1 3.8 - - - +
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Residues in contact with VAL 146 (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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54A CYS* 4.3 5.2 - - + -
55A ALA 3.3 26.7 - - - +
56A VAL* 4.1 8.7 - - + +
57A THR 4.2 0.7 - - - +
90A VAL* 3.6 32.5 - - + -
92A VAL* 5.9 5.3 - - + +
96A ASP 3.5 1.7 - - - +
97A GLU* 3.3 4.5 - - - +
98A VAL* 2.9 58.7 + - + +
100A LEU* 3.8 15.5 - - + -
121A VAL* 6.0 0.2 - - + -
144A ILE* 4.8 2.7 - - + +
145A LYS* 1.3 72.9 - - - +
147A GLN* 1.3 67.1 + - - +
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Residues in contact with GLN 147 (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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54A CYS* 3.6 6.4 - - - +
55A ALA 3.3 28.6 + - - +
57A THR* 3.4 25.7 + - - +
92A VAL* 6.1 0.2 - - - -
96A ASP 3.4 7.9 - - - +
97A GLU* 3.8 17.8 - - + +
145A LYS* 2.6 33.5 + - - +
146A VAL* 1.3 77.0 - - - +
148A ARG* 1.3 65.1 + - - +
158A ARG* 4.9 5.8 - - - +
177A TYR* 3.3 23.0 + - - +
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Residues in contact with ARG 148 (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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52A PRO* 5.4 9.9 - - + +
53A GLY* 3.9 12.9 + - - +
54A CYS* 3.3 16.6 - - - -
92A VAL* 2.6 51.3 + - - +
93A GLN 4.5 7.7 + - - -
94A GLY 4.9 0.8 + - - -
95A LYS 3.4 13.5 + - - -
96A ASP* 3.2 36.8 + - + +
97A GLU* 5.5 0.4 + - - -
147A GLN* 1.3 80.0 + - - +
149A GLY* 1.3 63.6 + - - +
177A TYR* 4.7 4.0 - - - -
6B THR* 5.3 12.8 - - + -
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Residues in contact with GLY 149 (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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52A PRO* 4.7 2.2 - - - -
53A GLY 2.5 37.9 + - - +
147A GLN 4.1 0.6 + - - -
148A ARG* 1.3 80.0 - - - +
150A ARG* 1.3 57.8 - - - -
177A TYR* 3.1 32.0 - - - +
6B THR* 5.8 5.2 - - - -
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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