Contacts of the strand formed by residues 41 - 50 (chain A) in PDB entry 1KKU
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LYS* 3.7 11.0 + - - +
7A THR* 3.2 28.7 - - + +
9A VAL* 3.5 26.0 - - + -
35A MET* 3.3 41.3 - - + +
36A ASN* 3.3 22.4 - - - +
38A THR* 3.2 18.4 + - + -
39A GLY 3.6 0.6 - - - -
40A ARG* 1.3 105.8 + - + +
42A THR* 1.3 67.9 + - - +
152A LYS* 4.3 16.4 + - - -
211A HIS* 3.5 21.0 + + - -
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Residues in contact with THR 42 (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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6A LYS* 3.2 27.3 + - - +
7A THR 2.8 12.2 + - - -
8A GLU* 3.4 11.9 - - + +
9A VAL 3.0 22.4 + - - -
36A ASN* 3.0 9.1 + - - +
41A TYR* 1.3 76.1 + - - +
43A VAL* 1.3 71.2 + - - +
44A VAL* 3.6 11.3 + - + +
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Residues in contact with VAL 43 (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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9A VAL* 3.7 15.5 - - + +
11A LEU* 4.4 11.0 - - + -
32A LYS* 3.7 42.0 + - + +
35A MET* 3.7 33.2 - - + -
36A ASN* 2.9 11.4 + - - +
42A THR* 1.3 77.9 - - - +
44A VAL* 1.3 65.8 + - - +
45A LYS 4.2 3.8 - - - +
79A TRP* 3.6 34.3 - - + -
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Residues in contact with VAL 44 (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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8A GLU* 3.5 36.8 - - + +
9A VAL 2.8 16.3 + - - +
10A VAL* 4.6 9.0 - - + -
42A THR* 4.2 12.3 - - + +
43A VAL* 1.3 81.0 - - - +
45A LYS* 1.3 69.9 + - + +
79A TRP* 5.0 7.9 - - - +
149A PRO* 5.1 8.5 - - + -
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Residues in contact with LYS 45 (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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9A VAL 3.9 2.1 + - - +
10A VAL* 3.4 15.6 - - + +
11A LEU* 3.0 23.2 + - - +
43A VAL* 3.8 2.1 - - - +
44A VAL* 1.3 89.3 - - + +
46A GLY* 1.3 69.9 + - - +
47A ILE* 3.7 24.9 - - + -
79A TRP* 3.6 17.9 - - - +
81A GLU* 3.3 34.7 + - - +
105A LYS* 5.8 5.7 - - - +
106A LEU* 4.9 15.7 - - - +
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Residues in contact with GLY 46 (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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11A LEU* 3.2 9.0 - - - -
28A PHE* 4.0 9.6 - - - -
45A LYS* 1.3 74.8 - - - +
47A ILE* 1.3 68.4 + - - +
79A TRP* 2.9 28.8 + - - +
80A VAL* 3.4 3.1 - - - -
81A GLU* 2.9 27.7 + - - +
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Residues in contact with ILE 47 (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* 3.4 28.0 - - + -
11A LEU 2.6 10.9 + - - +
12A LEU* 3.4 20.1 - - + +
13A ALA 2.8 31.7 + - - +
28A PHE* 3.8 6.8 - - - -
45A LYS* 3.7 24.9 - - - -
46A GLY* 1.3 79.6 - - - +
48A ILE* 1.3 68.5 + - - +
49A SER* 4.7 0.7 - - - +
81A GLU* 3.2 10.3 - - - +
83A ASP* 3.9 22.4 - - + -
102A HIS* 4.2 24.2 - - + +
106A LEU* 5.8 4.0 - - + -
151A VAL* 5.7 0.2 - - + -
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Residues in contact with ILE 48 (chain A).
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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13A ALA 3.5 5.4 - - - -
17A PHE* 3.4 29.8 - - + -
20A ILE* 3.7 25.8 - - + -
24A HIS* 5.9 0.4 - - + -
25A LEU* 4.6 4.3 - - + -
28A PHE* 3.7 26.5 - - + -
47A ILE* 1.3 75.2 - - - +
49A SER* 1.3 62.9 + - - +
50A PRO* 4.0 10.3 - - + +
70A ALA* 4.1 18.2 - - + -
74A THR* 3.9 23.8 - - + -
80A VAL* 4.1 9.0 - - + -
81A GLU 2.9 9.4 + - - +
82A VAL* 3.5 7.2 - - + -
83A ASP 3.3 23.4 + - - +
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Residues in contact with SER 49 (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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12A LEU* 4.2 18.4 - - - -
13A ALA 2.9 12.8 + - - -
14A CYS* 3.6 18.7 - - - -
15A GLY 3.8 0.5 + - - -
17A PHE* 4.0 2.7 - - - -
47A ILE* 4.7 2.9 - - - -
48A ILE* 1.3 75.6 - - - +
50A PRO* 1.3 68.8 + - - +
51A VAL 3.8 0.5 + - - -
83A ASP 3.7 11.4 + - - -
86A GLU* 3.0 36.3 + - - +
98A VAL* 4.2 4.7 - - - +
102A HIS* 4.6 6.0 + - - -
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Residues in contact with PRO 50 (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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15A GLY 3.3 7.0 - - - +
16A SER 4.5 2.7 - - - +
17A PHE* 3.7 20.2 - - + -
48A ILE* 3.9 13.5 - - + +
49A SER* 1.3 90.1 + - - +
51A VAL* 1.3 66.2 + - - +
63A ALA* 6.2 0.2 - - + -
66A ARG* 3.9 22.4 - - + +
67A VAL* 4.2 31.0 - - + -
70A ALA* 4.9 1.3 - - + -
82A VAL* 4.2 8.3 - - + -
83A ASP 4.0 9.4 - - - +
86A GLU* 3.6 13.0 - - - +
87A SER* 3.8 10.1 + - - -
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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