Contacts of the strand formed by residues 3 - 12 (chain K) in PDB entry 2NX5
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 HIS 3 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K GLY* 3.4 25.9 + - - -
2K SER* 1.3 79.2 + - - +
4K SER* 1.3 63.3 + - - +
29K ASP* 3.2 28.0 - - - +
102K ASP* 3.5 1.7 - - - +
103K LEU* 2.6 47.5 + - + +
104K GLY 5.5 1.0 + - - -
168K LEU* 4.5 2.2 - - + -
172K LEU* 3.7 36.5 - - + +
179K LEU 3.9 10.3 + - - -
180K GLN* 3.2 34.3 + - + -
264K GLU* 5.5 3.2 + - - -
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Residues in contact with SER 4 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K HIS* 1.3 80.2 - - - +
5K MET* 1.3 59.5 + - - +
6K ARG* 4.0 15.3 - - - +
28K VAL* 3.4 4.0 - - - -
29K ASP* 2.8 45.4 + - - +
101K CYS 3.3 6.3 - - - -
102K ASP* 3.7 22.9 - - - -
168K LEU* 3.8 9.6 - - - +
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Residues in contact with MET 5 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLU 3.7 28.3 - - - +
4K SER* 1.3 74.1 - - - +
6K ARG* 1.3 72.4 + - - +
7K TYR* 4.4 10.3 - - + -
27K TYR 3.3 10.8 - - - +
28K VAL* 4.6 5.4 - - + -
33K PHE* 4.6 3.4 - - + -
100K GLY* 3.1 24.4 - - - -
101K CYS 3.2 9.4 + - - -
159K TYR* 3.7 7.6 - - - +
163K LEU 4.9 1.3 - - - +
164K CYS* 3.6 39.7 - - - +
167K TRP* 4.9 1.3 - - + -
168K LEU* 3.5 23.0 - - + +
171K TYR* 3.7 32.1 - - - -
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Residues in contact with ARG 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K SER* 4.0 13.5 - - - +
5K MET* 1.3 76.6 + - - +
7K TYR* 1.3 66.6 + - - +
8K PHE* 3.5 31.7 - - + -
26K GLY* 3.4 2.6 - - - -
27K TYR* 2.7 43.3 + - + +
29K ASP 5.8 3.4 - - - +
98K MET* 5.5 3.1 - - - -
99K TYR* 3.4 21.8 - - - +
100K GLY* 3.6 14.3 - - - -
101K CYS 3.8 0.6 - - - +
102K ASP* 2.8 31.8 + - - -
113K HIS* 3.2 39.2 + - - +
58L LYS* 4.8 20.0 - - - +
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Residues in contact with TYR 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H GLU* 2.9 31.0 + - - -
2H PRO* 3.4 29.9 - - + +
5K MET* 4.4 12.8 - - + -
6K ARG* 1.3 77.2 - - - +
8K PHE* 1.3 63.2 + - - +
9K TYR* 4.3 5.8 - + + -
25K VAL 3.4 7.2 - - - -
26K GLY* 3.6 21.5 - - - -
33K PHE* 3.4 18.6 - + - -
34K VAL* 3.7 12.6 - - + +
63K ASN* 4.1 2.9 + - - -
67K PHE* 4.0 20.9 - + - -
97K ARG 3.7 0.9 - - - +
98K MET* 3.3 6.6 - - - +
99K TYR* 3.0 73.0 + + + +
159K TYR* 4.0 2.7 - - - -
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Residues in contact with PHE 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ARG* 3.5 34.8 - - + -
7K TYR* 1.3 76.4 - - - +
9K TYR* 1.3 64.3 + - - +
23K ILE 3.6 1.0 - - - +
24K ALA* 3.3 5.2 - - - -
25K VAL* 2.8 48.8 + - + +
27K TYR* 3.8 31.0 - + + -
97K ARG 3.4 3.4 - - - -
98K MET* 3.8 27.4 - - + -
55L SER* 4.2 4.3 - - - +
56L PHE* 3.6 49.8 - + + -
57L SER 5.2 2.5 - - - -
58L LYS* 5.6 2.9 - - + -
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Residues in contact with TYR 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H PRO* 4.2 2.8 - - - +
3H LEU 4.4 1.9 + - - -
5H GLN* 3.7 6.8 + - - -
7K TYR* 4.3 9.4 - + + -
8K PHE* 1.3 81.7 - - - +
10K THR* 1.3 66.3 + - - +
22K PHE* 3.8 13.7 - + + -
23K ILE 3.3 3.1 - - - +
24K ALA* 3.6 24.2 - - + -
67K PHE* 4.1 13.0 - + - -
70K ASN* 3.2 30.2 + - - -
74K TYR* 3.1 33.4 - + + -
95K ILE 4.4 0.7 - - - -
96K GLN* 3.4 5.9 - - - -
97K ARG* 2.7 46.9 + - + +
99K TYR* 2.8 42.5 + + - -
56L PHE* 3.4 4.9 - - - -
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Residues in contact with THR 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K TYR* 1.3 76.5 + - - +
11K ALA* 1.3 62.8 + - - +
12K MET* 3.5 34.1 - - + -
21K ARG 3.4 1.7 - - - +
22K PHE* 3.4 3.8 - - - -
23K ILE* 2.7 53.5 + - - +
94K ILE* 3.9 10.3 - - + -
95K ILE 3.6 3.1 - - - -
96K GLN* 4.5 0.8 - - + +
54L LEU* 4.4 6.4 + - + -
56L PHE* 3.2 23.2 - - - -
62L PHE* 3.7 20.3 - - + -
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Residues in contact with ALA 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K THR* 1.3 72.7 - - - +
12K MET* 1.3 62.7 + - - +
20K PRO* 5.8 0.2 - - + -
21K ARG 3.2 7.0 - - - +
22K PHE* 4.4 6.3 - - + +
74K TYR* 3.9 30.7 - - + -
78K LEU* 3.7 25.6 - - + +
93K HIS 3.7 1.4 - - - +
94K ILE* 3.4 5.0 - - - -
95K ILE* 3.1 34.0 + - + +
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Residues in contact with MET 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K THR* 3.5 24.9 - - + -
11K ALA* 1.3 71.2 - - - +
13K SER* 1.3 65.1 + - - +
14K ARG* 3.7 8.1 + - + +
17K ARG* 6.3 0.7 - - - +
20K PRO* 3.4 2.7 - - - +
21K ARG* 2.8 56.2 + - + +
23K ILE* 4.0 9.2 - - - -
93K HIS 3.8 3.4 - - - -
94K ILE* 3.7 17.3 - - + -
33L SER* 3.2 30.1 - - - +
34L ASP* 3.5 21.8 - - - +
54L LEU* 3.7 19.3 - - + -
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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