Contacts of the helix formed by residues 84 - 95 (chain A) in PDB entry 1KPI
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A CYS 2.9 16.0 + - - -
82A GLY 3.2 1.2 + - - -
83A TRP* 1.3 74.3 - - - +
85A SER* 1.3 62.6 + - - +
86A THR 3.2 2.9 - - - -
87A MET* 2.9 27.4 + - - +
88A ARG* 3.0 15.1 + - - +
111A ASP* 3.1 15.1 + - - -
115A PHE* 4.4 6.0 - - - -
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Residues in contact with SER 85 (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 SER* 3.5 21.5 - - - -
40A THR* 3.1 35.0 + - - +
61A ARG* 3.5 19.1 + - - -
81A CYS 4.7 0.4 + - - -
83A TRP 3.2 6.9 + - - -
84A GLY* 1.3 73.4 - - - +
86A THR* 1.3 66.8 + - - +
88A ARG* 3.4 8.7 + - - +
89A HIS* 2.9 31.9 + - - +
900A SAH 4.5 4.9 + - - -
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Residues in contact with THR 86 (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 THR* 5.8 0.3 - - - +
61A ARG* 3.9 14.6 - - + +
64A ALA* 6.3 0.2 - - + -
65A LEU* 4.4 20.6 - - + -
76A LEU* 5.5 0.7 - - + -
78A ASP* 3.3 19.9 + - + +
81A CYS 5.5 1.0 + - - -
84A GLY 3.2 1.0 - - - -
85A SER* 1.3 83.6 + - - +
87A MET* 1.3 58.6 + - - +
89A HIS* 3.7 1.5 - - - +
90A ALA* 2.8 28.7 + - + +
142A VAL* 4.2 21.1 - - + -
144A LEU* 3.4 29.0 - - + +
900A SAH 4.8 7.4 + - - -
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Residues in contact with MET 87 (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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76A LEU* 5.8 0.7 - - - -
78A ASP* 3.7 25.4 - - + +
81A CYS* 3.9 16.2 - - + -
84A GLY* 2.9 10.8 + - - +
86A THR* 1.3 76.4 - - - +
88A ARG* 1.3 64.7 + - - +
90A ALA* 3.1 15.5 + - - +
91A VAL* 3.1 18.9 + - - +
98A VAL* 3.9 26.0 - - + +
99A ILE 3.8 2.9 - - - -
100A GLY* 3.2 20.4 - - - +
111A ASP* 5.3 0.4 - - - +
115A PHE* 3.3 35.2 - - + -
125A GLU 2.9 31.4 - - - +
126A VAL* 4.8 3.4 - - - -
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Residues in contact with ARG 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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38A SER* 6.2 2.2 - - - +
84A GLY 3.0 10.0 + - - +
85A SER* 3.7 10.8 - - - +
87A MET* 1.3 78.2 - - - +
89A HIS* 1.3 61.2 + - - +
91A VAL* 3.7 4.6 + - - +
92A ALA* 3.2 26.7 + - + +
114A MET* 3.7 41.7 + - - +
115A PHE* 4.5 15.4 - - + -
117A GLU* 5.0 4.6 + - - +
118A VAL* 5.0 15.8 - - - +
124A LYS* 6.4 2.5 - - - +
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Residues in contact with HIS 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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58A TYR* 3.3 53.7 + + - -
61A ARG* 2.9 34.6 + - + +
62A LYS* 3.9 10.3 - - + +
65A LEU* 3.9 11.7 - - + -
85A SER 2.9 18.0 + - - +
86A THR* 3.7 3.6 - - - +
88A ARG* 1.3 75.6 - - - +
90A ALA* 1.3 59.2 + - - +
92A ALA* 4.7 3.6 - - - -
93A GLU* 2.9 50.1 + - + +
94A TYR* 4.0 7.0 + + - -
904A SO4 4.9 1.0 + - - -
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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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65A LEU* 3.8 16.4 - - + +
70A LEU* 5.3 0.4 - - + -
76A LEU* 3.3 32.5 - - + -
86A THR 2.8 18.6 + - - +
87A MET 3.1 4.7 + - - +
89A HIS* 1.3 77.2 - - - +
91A VAL* 1.3 57.7 + - - +
94A TYR* 3.0 35.7 + - + +
95A ASP 3.5 1.2 + - - -
96A VAL* 3.8 6.5 - - + +
98A VAL* 3.8 7.2 - - + -
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Residues in contact with VAL 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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87A MET 3.1 9.2 + - - +
88A ARG* 4.1 4.7 - - - +
90A ALA* 1.3 75.5 - - - +
92A ALA* 1.3 62.9 + - - +
95A ASP* 2.8 29.4 + - - +
96A VAL 3.5 24.5 - - - +
98A VAL* 3.4 33.7 - - + -
120A SER* 4.0 22.0 - - - +
122A ARG* 4.1 11.0 - - + -
123A ARG 4.5 1.8 - - - +
124A LYS* 4.3 24.2 - - + -
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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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88A ARG* 3.2 19.8 + - + +
89A HIS* 4.0 3.6 - - - +
91A VAL* 1.3 81.3 - - - +
93A GLU* 1.3 73.8 + - + +
95A ASP 5.0 0.3 + - - -
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Residues in contact with GLU 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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58A TYR* 3.5 25.6 + - + +
89A HIS* 2.9 34.1 + - + +
92A ALA* 1.3 91.7 - - + +
94A TYR* 1.3 82.0 + - + +
904A SO4 4.1 13.9 + - - +
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Residues in contact with TYR 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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62A LYS* 3.8 13.0 + - - +
65A LEU* 3.4 43.2 - - + +
66A ASP* 2.6 32.7 + - - -
70A LEU* 4.0 30.4 - - + +
71A GLU 4.3 0.5 - - - -
72A PRO* 3.7 19.3 - - - +
89A HIS* 4.0 5.2 + + - -
90A ALA* 3.0 22.5 + - - +
93A GLU* 1.3 98.2 - - + +
95A ASP* 1.3 73.7 + - - +
96A VAL* 3.5 14.5 + - + +
904A SO4 5.4 1.8 + - - -
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Residues in contact with ASP 95 (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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72A PRO* 3.3 16.0 - - + +
73A GLY 3.1 17.0 + - - -
90A ALA 3.5 0.2 + - - -
91A VAL* 2.8 19.4 + - - +
92A ALA 4.7 0.4 + - - -
93A GLU 3.8 0.4 - - - -
94A TYR* 1.3 80.8 - - - +
96A VAL* 1.3 58.4 + - - +
120A SER* 5.3 1.7 + - - -
121A PRO* 5.8 2.8 - - - +
122A ARG* 2.7 48.9 + - - +
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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