Contacts of the helix formed by residues 94 - 107 (chain A) in PDB entry 1KQN
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 GLU 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A TRP* 3.8 13.2 - - + -
93A LYS* 1.3 73.3 - - - +
95A THR* 1.3 56.3 + - - +
96A LEU* 4.2 4.3 - - + +
97A LYS* 2.6 68.6 + - + +
98A VAL* 3.1 8.3 + - - +
170A LYS* 4.4 16.5 + - + +
173A ASP* 3.6 22.7 - - - +
272A ARG* 2.9 39.5 + - - -
273A ASN* 4.9 4.6 - - - +
777A NAD 3.3 16.4 - - - +
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Residues in contact with THR 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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14A CYS* 4.0 13.5 - - + +
86A GLU* 5.4 0.6 + - - -
93A LYS 3.6 2.4 + - - -
94A GLU* 1.3 71.6 - - - +
96A LEU* 1.3 56.3 + - - -
98A VAL* 3.0 10.0 + - - -
99A LEU* 2.8 37.8 + - + +
153A LEU* 3.8 36.3 - - + -
159A LEU* 5.8 0.4 - - + +
169A TRP* 3.8 11.4 - - + -
177A ILE* 4.8 1.3 - - + -
777A NAD 2.7 51.7 + - - -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 3.0 3.0 + - + +
95A THR* 1.3 77.3 - - - +
97A LYS* 1.3 58.4 + - + +
99A LEU* 3.3 3.3 + - - +
100A ARG* 2.9 50.9 + - - +
173A ASP* 3.3 38.1 - - - +
176A GLN* 3.8 39.7 - - + +
177A ILE* 4.0 23.1 - - + +
181A TYR* 3.5 31.9 - - + -
777A NAD 4.3 1.0 + - - -
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TRP* 4.4 5.1 - - + -
93A LYS* 4.3 30.4 - - + +
94A GLU* 2.6 57.9 + - + +
96A LEU* 1.3 70.7 - - + +
98A VAL* 1.3 57.6 + - - +
100A ARG* 3.6 20.2 - - - +
101A HIS* 2.8 30.7 + - - +
170A LYS* 5.4 6.8 - - - +
272A ARG* 4.2 7.1 - - - +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 2.7 - - + -
14A CYS* 3.8 17.0 - - - -
49A SER* 4.4 3.1 - - - +
85A TRP* 3.9 25.4 - - + -
86A GLU* 3.5 40.2 - - + +
93A LYS* 4.4 6.7 - - + +
94A GLU 3.1 11.1 + - - +
95A THR* 3.0 10.6 + - - +
97A LYS* 1.3 75.9 - - - +
99A LEU* 1.3 63.8 + - - +
101A HIS* 3.2 0.7 + - - +
102A HIS* 3.0 51.1 + - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 14.1 - - + -
95A THR* 2.8 28.2 + - + +
96A LEU* 3.5 7.2 - - - +
98A VAL* 1.3 76.9 - - - +
100A ARG* 1.3 57.4 + - - +
102A HIS* 3.2 3.5 + - - +
103A GLN* 2.9 29.5 + - - +
151A VAL* 4.0 25.7 - - + +
153A LEU* 4.0 25.4 - - + +
177A ILE* 3.9 37.9 - - + -
181A TYR* 3.9 33.6 - - + -
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Residues in contact with ARG 100 (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 LEU* 2.9 47.0 + - - +
97A LYS* 3.6 20.0 - - - +
99A LEU* 1.3 76.0 - - - +
101A HIS* 1.3 54.1 + - - +
103A GLN* 3.2 0.7 + - - +
104A GLU* 2.8 63.7 + - + +
176A GLN* 3.3 25.3 + - - +
181A TYR* 3.4 23.9 + - - +
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Residues in contact with HIS 101 (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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83A ASP* 4.9 0.6 + - - -
85A TRP* 3.1 67.9 + + + +
97A LYS 2.8 21.4 + - - +
98A VAL 3.4 4.7 - - - +
100A ARG* 1.3 73.2 - - - +
102A HIS* 1.3 81.0 + + - +
104A GLU* 3.5 11.0 + - - +
105A LYS* 3.0 41.4 + - + +
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Residues in contact with HIS 102 (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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10A VAL* 6.4 0.2 - - + -
12A LEU* 3.9 14.9 - - + +
47A ILE* 3.8 25.8 - - + +
49A SER* 4.9 2.4 + - - -
83A ASP* 3.4 43.5 + - + +
85A TRP* 5.1 1.6 - - - +
86A GLU* 6.4 0.2 - - - +
98A VAL* 3.0 48.3 + - + +
99A LEU 3.8 3.4 - - - +
101A HIS* 1.3 87.5 - + - +
103A GLN* 1.3 61.3 + - - +
105A LYS* 3.2 14.8 + - - +
106A LEU* 2.9 32.0 + - + +
151A VAL* 3.9 18.6 - - + -
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Residues in contact with GLN 103 (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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99A LEU 2.9 16.3 + - - +
100A ARG* 3.7 3.8 - - - +
102A HIS* 1.3 76.0 - - - +
104A GLU* 1.3 58.0 + - + +
106A LEU* 3.1 4.3 + - - +
107A GLU* 2.7 48.5 + - - +
148A VAL* 3.7 13.9 - - - +
149A PRO 3.1 22.0 + - - -
150A LYS* 3.6 7.6 - - - +
151A VAL* 2.9 36.3 + - + +
181A TYR* 3.8 22.9 - - + +
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Residues in contact with GLU 104 (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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100A ARG* 2.8 47.9 + - + +
101A HIS* 3.9 10.7 + - - +
103A GLN* 1.3 73.4 - - + +
105A LYS* 1.3 63.5 + - - +
107A GLU* 3.4 27.9 + - - +
108A ALA* 3.6 7.6 + - - +
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Residues in contact with LYS 105 (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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47A ILE* 6.0 1.8 - - - +
83A ASP* 3.1 26.1 + - - -
101A HIS* 3.0 31.3 + - + +
102A HIS* 3.3 20.3 - - - +
103A GLN 3.1 0.2 - - - -
104A GLU* 1.3 74.9 - - - +
106A LEU* 1.3 66.7 + - + +
108A ALA* 2.9 24.6 + - + +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.8 23.8 - - + -
45A LYS* 4.1 22.9 - - - +
47A ILE* 6.4 0.2 - - + -
102A HIS* 2.9 14.7 + - + +
103A GLN* 3.1 6.9 + - - +
105A LYS* 1.3 78.2 - - + +
107A GLU* 1.3 63.0 + - - +
108A ALA 3.0 10.8 + - - +
148A VAL* 3.9 19.6 - - + +
149A PRO* 3.3 35.4 - - + +
151A VAL* 3.4 26.5 - - + -
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 2.7 50.0 + - - +
104A GLU* 3.4 17.9 - - - +
105A LYS 3.1 0.2 - - - -
106A LEU* 1.3 75.8 - - - +
108A ALA* 1.3 58.0 + - - +
148A VAL* 4.2 22.5 - - + +
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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