Contacts of the strand formed by residues 87 - 94 (chain A) in PDB entry 3KAP
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 LYS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP* 3.3 15.7 + - + +
52A ALA* 3.3 10.5 - - + -
53A VAL* 3.0 23.7 + - - +
85A GLY 5.0 1.3 - - - +
86A LYS* 1.3 77.8 - - - +
88A LEU* 1.3 61.5 + - - +
118A GLU* 3.3 33.2 - - - +
120A ILE* 3.5 21.1 - - + -
147A LYS 2.8 29.0 + - - +
148A LEU* 3.6 26.5 + - + +
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Residues in contact with LEU 88 (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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53A VAL* 3.2 15.9 - - + +
54A LEU* 5.0 1.6 - - - -
55A MET* 4.0 32.3 - - + -
78A MET* 5.6 0.2 - - - -
83A LEU* 4.4 15.5 - - + -
86A LYS* 6.1 0.2 - - + -
87A LYS* 1.3 77.8 - - - +
89A ALA* 1.3 76.5 + - - +
90A ALA* 4.4 2.5 - - + +
108A ILE* 4.1 15.7 - - + +
109A GLU* 4.9 3.1 - - + -
112A ALA* 3.8 28.9 - - + -
117A ALA* 4.4 11.2 - - + -
118A GLU 2.8 10.6 + - - +
119A VAL* 3.1 17.6 - - + +
120A ILE* 2.8 29.1 + - - +
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Residues in contact with ALA 89 (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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53A VAL 3.2 5.6 + - - +
54A LEU* 3.2 21.1 - - + +
55A MET 3.0 24.6 + - - +
88A LEU* 1.3 83.9 - - - +
90A ALA* 1.3 60.5 + - - +
91A PHE* 5.2 0.2 - - - -
119A VAL* 5.4 0.7 - - - -
120A ILE* 4.4 14.4 - - + -
121A CYS* 4.6 11.0 - - - +
140A PHE* 3.7 26.2 - - + -
144A VAL* 4.6 1.8 - - + -
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Residues in contact with ALA 90 (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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55A MET 3.1 9.6 - - - +
88A LEU* 4.4 1.2 - - + +
89A ALA* 1.3 74.3 - - - +
91A PHE* 1.3 63.9 + - - +
105A VAL* 4.2 28.3 - - + +
108A ILE* 4.1 23.1 - - + -
109A GLU* 4.2 13.5 + - + +
121A CYS 5.2 0.2 + - - -
123A GLY* 2.9 26.1 - - - -
124A LEU 2.9 3.5 + - - -
140A PHE* 3.5 5.9 - - - -
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Residues in contact with PHE 91 (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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6A ILE* 3.9 21.5 - - + -
7A LEU 4.0 6.3 - - - -
8A PHE* 4.3 1.3 - - + -
15A THR* 3.7 35.4 - - + -
18A ILE* 3.7 16.4 - - + -
19A ALA* 4.0 13.5 - - + -
22A LEU* 4.0 13.5 - - + -
54A LEU* 3.6 24.5 - - + -
55A MET 3.1 21.7 + - - -
56A GLY* 2.9 32.4 - - - -
57A CYS 3.4 0.7 + - - -
89A ALA 4.7 0.2 - - - -
90A ALA* 1.3 76.5 - - - +
92A ALA* 1.3 63.8 + - - +
104A ALA* 5.5 0.2 - - - +
105A VAL* 3.8 3.9 - - - +
108A ILE* 5.3 1.2 - - - +
124A LEU* 3.3 31.0 - - + -
140A PHE* 4.4 6.1 - + + -
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Residues in contact with ALA 92 (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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15A THR* 4.5 3.8 - - - -
18A ILE* 3.8 10.9 - - - +
57A CYS 3.2 25.6 - - - +
91A PHE* 1.3 77.0 - - - +
93A SER* 1.3 64.8 + - - +
102A CYS* 3.8 19.6 - - + +
104A ALA* 4.9 0.2 - - + -
105A VAL* 3.7 19.1 - - + +
124A LEU* 3.0 7.0 + - - +
126A ILE* 3.1 24.6 + - - +
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Residues in contact with SER 93 (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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14A ASN* 3.2 13.2 - - - +
15A THR* 3.4 20.9 + - - -
18A ILE* 3.8 10.0 - - - +
58A SER* 3.7 23.9 - - - -
59A ALA 4.7 0.5 + - - -
92A ALA* 1.3 78.0 - - - +
94A GLY* 1.3 59.1 + - - +
102A CYS* 3.9 3.5 - - - -
126A ILE 3.3 5.4 - - - -
128A GLY 2.6 30.6 + - - -
150A FMN 2.8 23.6 + - - -
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Residues in contact with GLY 94 (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 SER* 1.3 76.0 + - - +
95A ASP* 1.3 59.6 + - - +
101A TYR* 3.7 5.2 - - - -
102A CYS* 3.7 8.6 - - - -
126A ILE 2.8 7.7 + - - -
127A GLU* 3.2 22.0 - - - +
128A GLY 3.5 5.9 + - - -
150A FMN 3.4 31.3 + - - -
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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