Contacts of the strand formed by residues 41 - 50 (chain C) in PDB entry 1KR2
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C LYS* 4.0 10.5 + - - +
7C THR* 3.2 34.3 - - + +
9C VAL* 3.7 19.7 - - + -
35C MET* 3.4 46.0 - - + +
36C ASN* 3.4 21.1 - - - +
38C THR* 3.5 18.2 + - + -
40C ARG* 1.3 104.9 + - + +
42C THR* 1.3 67.8 + - - +
152C LYS* 5.0 9.2 + - - -
208C SER 4.9 2.3 + - - -
209C ASN* 5.7 1.2 + - - -
211C HIS* 3.5 27.1 + + - -
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Residues in contact with THR 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LYS* 3.6 22.7 + - - +
7C THR 3.0 9.2 + - - -
8C GLU* 3.2 15.2 - - + +
9C VAL 2.8 29.9 + - - -
36C ASN* 3.3 6.5 - - - +
41C TYR* 1.3 76.1 + - - +
43C VAL* 1.3 61.3 + - - +
44C VAL* 3.3 16.8 + - + +
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 3.4 18.8 - - + +
11C LEU* 3.9 16.6 - - + -
32C LYS* 3.9 35.1 + - + -
35C MET* 3.7 33.0 - - + -
36C ASN* 2.8 17.0 + - - +
42C THR* 1.3 76.2 - - - +
44C VAL* 1.3 60.8 + - - +
45C LYS 4.1 2.2 - - - +
79C TRP* 3.6 34.6 - - + +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLU* 3.8 27.4 - - + +
9C VAL 2.8 21.3 + - - +
10C VAL* 3.9 17.0 - - + -
42C THR* 3.3 17.9 + - + +
43C VAL* 1.3 76.0 - - - +
45C LYS* 1.3 64.1 + - + +
79C TRP* 4.9 9.1 - - - +
149C PRO* 4.4 16.2 - - + -
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Residues in contact with LYS 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL 3.7 0.9 + - - +
10C VAL* 3.3 19.4 - - + +
11C LEU* 2.9 26.9 + - - +
43C VAL* 3.6 4.0 - - - +
44C VAL* 1.3 87.1 - - + +
46C GLY* 1.3 67.8 + - - +
47C ILE* 3.7 27.7 - - + +
79C TRP* 3.6 19.5 - - - +
81C GLU* 3.3 29.5 + - - +
105C LYS* 5.6 8.5 - - - +
106C LEU* 4.6 15.6 - - - +
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.4 6.1 - - - -
28C PHE* 3.6 16.6 - - - -
45C LYS* 1.3 77.8 - - - +
47C ILE* 1.3 61.9 + - - +
79C TRP* 2.9 25.4 + - - +
80C VAL* 3.4 3.1 - - - -
81C GLU* 2.8 30.3 + - - +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C VAL* 3.8 22.0 - - + -
11C LEU 2.7 12.7 + - - +
12C LEU* 3.5 20.3 - - + +
13C ALA 2.9 27.5 + - - -
28C PHE* 3.5 4.7 - - - -
45C LYS* 3.7 24.7 - - + +
46C GLY* 1.3 78.5 - - - +
48C ILE* 1.3 66.3 + - - +
49C SER* 4.6 0.2 - - - -
81C GLU* 3.3 8.7 - - + +
82C VAL 4.9 0.2 - - - -
83C ASP* 3.7 30.3 - - + +
102C HIS* 3.7 26.2 - - + +
105C LYS* 5.8 2.2 - - - +
106C LEU* 6.3 1.1 - - + -
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ALA 3.8 3.4 - - - -
17C PHE* 3.8 30.7 - - + -
20C ILE* 3.5 25.6 - - + -
24C HIS 5.5 1.3 - - - +
25C LEU* 4.1 5.6 - - + -
28C PHE* 3.6 29.6 - - + -
47C ILE* 1.3 71.2 - - - +
49C SER* 1.3 62.5 + - - +
50C PRO* 3.5 6.0 - - + +
70C ALA* 4.1 21.1 - - + -
74C THR* 3.9 22.0 - - + -
80C VAL* 4.0 8.1 - - + -
81C GLU 2.8 12.6 + - - +
82C VAL* 3.3 6.9 - - + -
83C ASP 2.9 24.3 + - - -
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Residues in contact with SER 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 3.8 24.5 - - - -
13C ALA 3.0 11.4 + - - -
14C CYS* 3.7 0.8 - - - -
15C GLY 3.7 14.4 + - - -
17C PHE* 4.1 1.8 - - - -
47C ILE* 4.6 3.4 - - - -
48C ILE* 1.3 74.0 - - - +
50C PRO* 1.3 66.7 - - - +
51C VAL 3.5 1.2 + - - -
83C ASP* 3.7 13.0 + - - -
86C GLU* 2.6 45.8 + - - +
98C VAL* 4.2 3.7 - - - +
102C HIS* 4.8 3.1 + - - -
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Residues in contact with PRO 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY 3.5 7.6 - - - +
16C SER 4.5 2.0 - - - +
17C PHE* 3.8 16.8 - - + -
48C ILE* 3.5 15.0 - - + +
49C SER* 1.3 88.2 - - - +
51C VAL* 1.3 65.2 + - - +
66C ARG* 4.1 19.7 - - + +
67C VAL* 4.3 26.7 - - + -
70C ALA* 4.3 13.7 - - + -
82C VAL* 4.1 7.0 - - + -
83C ASP 3.8 9.8 - - - +
86C GLU* 3.5 3.9 - - - +
87C SER* 3.4 20.8 + - - -
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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