Contacts of the strand formed by residues 41 - 50 (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 TYR 41 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LYS* 4.0 10.9 + - - +
7F THR* 3.4 31.9 - - + +
9F VAL* 4.5 10.3 - - + -
35F MET* 3.6 52.3 - - + +
36F ASN* 3.8 20.1 - - - +
38F THR* 3.2 27.7 + - + -
39F GLY 3.3 1.2 + - - -
40F ARG* 1.3 108.3 - - + +
42F THR* 1.3 68.2 + - - +
152F LYS* 4.8 13.5 + - - -
208F SER 5.0 0.9 + - - -
209F ASN* 5.6 0.9 + - - -
211F HIS* 3.3 26.7 + + - -
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Residues in contact with THR 42 (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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6F LYS* 3.4 24.4 + - - +
7F THR 3.1 8.7 + - - -
8F GLU* 3.4 12.7 - - - +
9F VAL* 3.0 24.9 + - - -
36F ASN* 3.5 5.4 - - - +
41F TYR* 1.3 79.2 + - - +
43F VAL* 1.3 66.8 + - - +
44F VAL* 3.3 17.1 + - + +
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Residues in contact with VAL 43 (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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9F VAL* 3.4 15.0 - - + +
11F LEU* 3.7 32.1 - - + -
32F LYS* 3.8 34.9 + - + -
35F MET* 3.6 28.5 - - + -
36F ASN* 2.9 20.3 + - - +
42F THR* 1.3 74.4 - - - +
44F VAL* 1.3 62.6 + - - +
45F LYS 4.2 2.0 - - - +
79F TRP* 3.8 21.0 - - + +
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Residues in contact with VAL 44 (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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8F GLU* 3.8 32.5 - - + +
9F VAL 2.8 22.3 + - - +
10F VAL* 3.5 19.3 - - + -
42F THR* 3.4 20.6 - - + +
43F VAL* 1.3 75.3 - - - +
45F LYS* 1.3 70.0 + - + +
79F TRP* 4.7 9.7 - - - +
149F PRO* 4.3 12.1 - - + -
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Residues in contact with LYS 45 (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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9F VAL 4.1 0.7 - - - +
10F VAL* 3.4 18.6 - - + +
11F LEU* 3.0 24.3 + - - -
43F VAL* 3.7 3.4 - - - +
44F VAL* 1.3 87.7 - - + +
46F GLY* 1.3 66.9 + - - +
47F ILE* 4.5 13.5 - - + +
79F TRP* 3.6 24.8 - - - +
81F GLU* 3.6 31.5 + - + +
106F LEU* 4.0 24.7 - - - +
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Residues in contact with GLY 46 (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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11F LEU* 3.5 6.5 - - - -
28F PHE* 3.7 8.7 - - - -
45F LYS* 1.3 75.0 - - - +
47F ILE* 1.3 60.4 + - - -
79F TRP* 3.0 28.5 + - - -
80F VAL* 3.3 8.2 - - - -
81F GLU* 2.9 32.1 + - - +
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Residues in contact with ILE 47 (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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10F VAL* 3.8 26.5 - - + -
11F LEU 2.8 11.9 + - - +
12F LEU* 3.7 19.5 - - + -
13F ALA 3.0 25.8 + - - +
28F PHE* 3.4 7.2 - - - -
45F LYS* 4.5 17.0 - - + +
46F GLY* 1.3 76.4 - - - +
48F ILE* 1.3 65.8 + - - +
49F SER* 4.6 0.2 - - - -
81F GLU* 3.4 11.2 - - - +
82F VAL 4.9 0.7 - - - -
83F ASP* 3.7 29.6 - - + +
102F HIS* 3.5 27.6 - - + +
105F LYS* 6.1 1.8 - - + +
106F LEU* 6.3 2.0 - - + -
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Residues in contact with ILE 48 (chain F).
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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13F ALA 3.8 2.7 - - - -
17F PHE* 3.8 33.7 - - + -
20F ILE* 3.6 23.1 - - + -
25F LEU* 4.2 5.2 - - + -
28F PHE* 3.6 25.6 - - + -
47F ILE* 1.3 72.9 - - - +
49F SER* 1.3 62.8 + - - +
50F PRO* 3.7 12.1 - - + +
70F ALA* 4.3 8.3 - - + -
74F THR* 3.6 30.5 - - + -
80F VAL* 3.9 9.6 - - + -
81F GLU 2.8 11.5 + - - +
82F VAL* 3.4 10.6 - - + -
83F ASP 2.9 25.3 + - - +
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Residues in contact with SER 49 (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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12F LEU* 4.0 18.6 - - - -
13F ALA 3.0 13.7 + - - -
14F CYS* 3.6 3.5 - - - -
15F GLY 3.5 17.1 + - - -
17F PHE* 4.4 2.0 - - - -
47F ILE* 4.6 3.1 - - - -
48F ILE* 1.3 77.5 - - - +
50F PRO* 1.3 64.8 - - - +
83F ASP* 3.6 12.7 + - - -
86F GLU* 2.4 46.4 + - - +
98F VAL* 4.0 4.4 - - - +
102F HIS* 4.9 0.7 - - - -
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Residues in contact with PRO 50 (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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15F GLY 3.3 7.9 - - - +
16F SER 4.5 3.8 - - - +
17F PHE* 4.0 7.2 - - + -
48F ILE* 3.7 18.2 - - + +
49F SER* 1.3 88.0 - - - +
51F VAL* 1.3 64.4 + - - +
66F ARG* 3.8 27.8 - - + +
67F VAL* 4.4 29.6 - - + -
70F ALA* 4.5 3.8 - - + -
82F VAL* 4.1 6.1 - - + -
83F ASP 3.8 9.9 - - - +
86F GLU* 3.9 4.2 - - - +
87F SER* 3.7 21.7 + - - -
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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
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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