Contacts of the strand formed by residues 41 - 50 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D LYS* 4.0 7.7 + - - +
7D THR* 3.4 30.7 - - + +
9D VAL* 4.0 12.8 - - + -
35D MET* 3.3 50.7 + - + +
36D ASN* 3.3 22.0 - - - +
38D THR* 3.2 23.9 + - + -
39D GLY 3.6 0.4 - - - -
40D ARG* 1.3 104.9 + - + +
42D THR* 1.3 66.0 + - - +
152D LYS* 4.9 14.8 + - - -
208D SER 5.2 1.7 + - - -
209D ASN* 5.5 2.1 + - - -
211D HIS* 3.8 24.7 + + - -
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Residues in contact with THR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LYS* 3.5 25.1 + - - +
7D THR 3.0 9.2 + - - -
8D GLU* 3.2 15.4 - - - +
9D VAL* 2.9 23.6 + - - -
36D ASN* 3.3 6.1 - - - +
41D TYR* 1.3 77.0 + - - +
43D VAL* 1.3 67.8 + - - +
44D VAL* 3.3 16.2 + - + +
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Residues in contact with VAL 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.5 14.1 - - + +
11D LEU* 4.1 15.0 - - + -
32D LYS* 3.8 36.2 + - + -
35D MET* 3.9 25.1 - - + -
36D ASN* 2.9 16.9 + - - +
42D THR* 1.3 75.1 - - - +
44D VAL* 1.3 63.0 + - - +
45D LYS 3.9 12.1 - - - +
79D TRP* 3.6 32.5 - - + +
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Residues in contact with VAL 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLU* 3.6 30.3 - - + +
9D VAL 3.0 15.6 + - - +
10D VAL* 4.0 15.9 - - + -
42D THR* 3.7 20.4 - - + +
43D VAL* 1.3 75.0 - - - +
45D LYS* 1.3 67.7 + - + +
79D TRP* 4.9 8.0 - - - +
149D PRO* 4.2 18.2 - - + -
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL 3.7 0.6 + - - -
10D VAL* 3.4 18.4 - - + +
11D LEU 3.0 23.6 + - - -
43D VAL* 3.5 7.8 - - - +
44D VAL* 1.3 87.4 - - + +
46D GLY* 1.3 67.9 + - - +
47D ILE* 3.8 27.3 - - + +
79D TRP* 3.7 20.0 - - - +
81D GLU* 3.4 28.1 + - - +
105D LYS* 6.3 1.0 - - - +
106D LEU* 4.0 24.4 - - - +
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Residues in contact with GLY 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU 3.4 6.5 - - - -
28D PHE* 3.7 16.8 - - - -
45D LYS* 1.3 73.2 - - - +
47D ILE* 1.3 63.4 + - - +
79D TRP* 2.9 24.3 + - - +
80D VAL* 3.4 2.9 - - - -
81D GLU* 2.7 34.1 + - - +
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 3.6 22.7 - - + -
11D LEU 2.7 11.4 + - - +
12D LEU* 3.5 22.8 - - + +
13D ALA 2.7 32.1 + - - -
28D PHE* 3.6 4.1 - - - -
45D LYS* 3.8 23.6 - - + +
46D GLY* 1.3 78.6 - - - +
48D ILE* 1.3 64.0 + - - +
81D GLU* 3.3 9.0 - - + +
82D VAL 4.9 0.4 - - - -
83D ASP* 3.5 29.8 - - + +
102D HIS* 3.9 22.4 - - + +
106D LEU* 6.3 1.3 - - + -
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Residues in contact with ILE 48 (chain D).
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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13D ALA 3.8 3.8 - - - -
17D PHE* 3.8 31.9 - - + -
20D ILE* 3.6 27.4 - - + -
24D HIS* 5.7 0.7 - - + -
25D LEU* 4.5 4.0 - - + -
28D PHE* 3.5 30.3 - - + -
47D ILE* 1.3 72.7 - - - +
49D SER* 1.3 56.3 + - - +
50D PRO* 3.4 11.0 - - + +
70D ALA* 4.1 16.8 - - + -
74D THR* 4.0 22.2 - - + -
80D VAL* 4.0 6.3 - - + -
81D GLU 2.8 11.9 + - - +
82D VAL* 3.3 5.5 - - + -
83D ASP 2.8 29.6 + - - -
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Residues in contact with SER 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.0 20.6 - - - -
13D ALA 3.0 14.0 + - - -
14D CYS* 3.6 4.2 - - - -
15D GLY 3.6 17.2 + - - -
17D PHE* 4.3 1.8 - - - -
47D ILE* 3.8 2.2 + - - -
48D ILE* 1.3 70.1 - - - +
50D PRO* 1.3 67.3 - - - +
51D VAL 3.5 1.2 + - - -
83D ASP* 3.6 11.4 + - - -
86D GLU* 2.5 42.8 + - - +
98D VAL* 3.7 5.3 - - - +
102D HIS* 5.0 2.0 + - - -
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Residues in contact with PRO 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY 3.5 7.0 - - - +
16D SER 4.8 0.2 - - - +
17D PHE* 3.9 8.7 - - + -
48D ILE* 3.4 24.7 - - + +
49D SER* 1.3 87.0 - - - +
51D VAL* 1.3 63.4 + - - +
66D ARG* 4.0 18.2 - - + +
67D VAL* 4.1 37.5 - - + +
70D ALA* 4.5 6.7 - - + -
82D VAL* 4.1 6.5 - - + -
83D ASP 3.7 10.2 - - - +
84D THR* 5.4 0.7 - - - -
86D GLU* 3.8 9.2 - - - +
87D SER* 3.7 15.2 + - - +
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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