Contacts of the helix formed by residues 94 - 107 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F TRP* 3.7 18.8 - - + -
93F LYS* 1.3 75.5 - - - +
95F THR* 1.3 65.5 + - - +
96F LEU* 4.2 4.9 - - + +
97F LYS* 3.1 44.3 + - + +
98F VAL* 3.1 9.9 + - - +
170F LYS* 3.9 18.8 + - + +
173F ASP* 3.7 21.5 - - - +
272F ARG* 2.9 42.1 + - - -
273F ASN* 4.7 5.7 - - - +
782F NAD 3.3 12.3 - - - +
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F CYS* 4.1 17.2 - - + +
86F GLU* 5.5 0.3 + - - -
93F LYS 3.6 1.4 + - - -
94F GLU* 1.3 69.0 - - - +
96F LEU* 1.3 64.4 + - - +
98F VAL* 3.1 8.4 + - - +
99F LEU* 2.8 29.7 + - + +
153F LEU* 3.9 37.9 - - + -
159F LEU* 6.0 1.5 - - + +
169F TRP* 3.9 11.6 - - + -
177F ILE* 4.7 1.3 - - + -
782F NAD 2.7 49.2 + - - -
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Residues in contact with LEU 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLU* 3.2 3.2 - - + +
95F THR* 1.3 77.4 - - - +
97F LYS* 1.3 61.8 + - + +
99F LEU* 2.9 7.9 + - + +
100F ARG* 2.8 54.6 + - - +
173F ASP* 3.5 46.0 - - + +
176F GLN* 3.9 26.9 - - + +
177F ILE* 4.2 20.7 - - + +
181F TYR* 3.6 29.8 - - + -
782F NAD 4.4 1.4 + - - -
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Residues in contact with LYS 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F TRP* 4.6 4.1 - - + -
93F LYS* 4.4 26.6 - - + +
94F GLU* 3.1 47.3 + - + +
96F LEU* 1.3 79.0 - - + +
98F VAL* 1.3 56.6 + - - +
100F ARG* 3.5 23.9 - - - +
101F HIS* 2.9 30.8 + - - +
170F LYS* 4.8 11.0 - - - +
272F ARG* 4.3 6.9 - - - +
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 4.1 2.2 - - + -
14F CYS* 3.6 17.3 - - - -
49F SER* 4.0 5.8 - - - +
85F TRP* 4.4 7.2 - - + -
86F GLU* 3.5 45.3 - - + +
93F LYS* 3.9 15.3 - - + +
94F GLU 3.2 16.2 - - - +
95F THR* 3.1 10.0 + - - +
97F LYS* 1.3 77.1 - - - +
99F LEU* 1.3 61.5 + - - +
101F HIS* 3.6 3.6 + - - +
102F HIS* 2.9 48.4 + - + +
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 3.7 23.1 - - + +
95F THR* 2.8 26.5 + - + +
96F LEU* 3.2 7.0 - - - +
98F VAL* 1.3 74.9 - - - +
100F ARG* 1.3 65.6 + - - +
102F HIS* 3.2 5.2 + - - +
103F GLN* 3.0 22.3 + - - +
151F VAL* 3.7 22.7 - - + +
153F LEU* 4.2 28.9 - - + +
177F ILE* 3.8 37.2 - - + -
181F TYR* 3.9 26.7 - - + -
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Residues in contact with ARG 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F LEU* 2.8 34.5 + - - +
97F LYS* 3.5 36.7 - - - +
99F LEU* 1.3 76.2 - - - +
101F HIS* 1.3 63.4 + - - +
103F GLN* 2.9 3.7 + - - +
104F GLU* 2.8 53.4 + - + +
176F GLN* 3.4 24.2 + - - +
181F TYR* 3.5 22.5 + - - +
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Residues in contact with HIS 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F ASP* 4.9 1.4 + - - -
85F TRP* 3.4 68.0 - + + +
97F LYS 2.9 18.4 + - - +
98F VAL 3.7 3.6 - - - +
100F ARG* 1.3 76.0 - - - +
102F HIS* 1.3 82.9 + + - +
104F GLU* 3.5 11.3 + - - +
105F LYS* 2.8 41.0 + - + +
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Residues in contact with HIS 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F VAL* 6.2 0.2 - - + -
12F LEU* 4.1 12.0 - - + +
47F ILE* 3.5 28.4 - - + +
49F SER* 4.9 1.8 + - - -
83F ASP* 3.2 44.2 + - + -
85F TRP* 5.0 1.6 - - - -
86F GLU 5.8 0.2 + - - -
98F VAL* 2.9 38.2 + - + +
99F LEU 3.2 7.9 + - - +
100F ARG 3.2 0.8 - - - -
101F HIS* 1.3 90.6 - + - +
103F GLN* 1.3 62.7 + - - +
105F LYS* 3.7 17.2 - - + +
106F LEU* 3.3 29.3 + - - +
151F VAL* 4.4 16.4 - - + -
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Residues in contact with GLN 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F LEU 3.0 11.8 + - - +
100F ARG* 2.9 8.8 + - - +
102F HIS* 1.3 75.0 - - - +
104F GLU* 1.3 69.2 + - + +
106F LEU* 2.9 17.7 + - - +
107F GLU* 3.3 29.3 + - - +
148F VAL* 4.0 12.7 + - - +
149F PRO 3.3 22.2 + - - -
150F LYS* 4.0 5.5 - - - +
151F VAL* 3.0 38.9 + - + +
180F ASN 5.6 0.3 - - - +
181F TYR* 4.0 16.5 - - + +
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Residues in contact with GLU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F ARG* 2.8 44.7 + - + +
101F HIS* 3.8 10.1 - - - +
103F GLN* 1.3 77.5 - - + +
105F LYS* 1.3 64.1 + - - +
107F GLU* 3.1 29.3 + - - +
108F ALA* 3.9 4.2 + - - +
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Residues in contact with LYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 6.1 2.7 - - + +
81F GLU* 5.7 3.0 + - - -
83F ASP* 4.0 19.0 + - - +
101F HIS* 2.8 31.8 + - + +
102F HIS* 3.7 20.9 + - + +
103F GLN 3.1 0.2 - - - -
104F GLU* 1.3 76.4 - - - +
106F LEU* 1.3 57.6 + - + +
107F GLU 2.7 11.8 + - - -
108F ALA* 2.9 25.6 + - + +
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F VAL* 4.0 30.3 - - + -
45F LYS* 4.0 24.5 - - - +
47F ILE* 6.3 2.0 - - + -
102F HIS* 3.3 15.2 + - + +
103F GLN* 2.9 13.2 + - - +
105F LYS* 1.3 82.3 - - + +
107F GLU* 1.3 57.9 + - - +
108F ALA 3.3 7.2 + - - +
148F VAL* 3.6 22.1 - - + +
149F PRO* 3.6 32.7 - - + +
151F VAL* 4.7 8.3 - - + -
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F GLN* 3.3 30.3 + - - +
104F GLU* 3.5 23.9 + - - +
105F LYS 2.7 4.6 + - - -
106F LEU* 1.3 76.7 - - - +
108F ALA* 1.3 59.3 + - - +
148F VAL* 3.9 24.7 - - + +
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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
------------------------------------------------------------
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