Contacts of the strand formed by residues 21 - 28 (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 ARG 21 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K THR 3.4 2.4 - - - +
11K ALA* 3.2 4.3 - - - -
12K MET* 2.8 57.9 + - + +
14K ARG* 3.4 36.3 - - - +
19K GLU 3.5 1.2 + - - -
20K PRO* 1.3 71.0 - - - +
22K PHE* 1.3 57.1 + - - +
23K ILE* 3.2 30.7 - - + +
37K ASP* 2.8 42.9 + - - +
38K SER* 3.3 15.9 - - - +
39K ASP* 2.8 30.9 + - - +
54L LEU* 5.1 9.9 - - - +
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Residues in contact with PHE 22 (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* 3.8 32.5 - + + -
10K THR 3.4 5.2 - - - -
11K ALA* 4.4 4.5 - - + +
20K PRO 3.7 2.3 + - - +
21K ARG* 1.3 72.9 - - - +
23K ILE* 1.3 66.1 + - - +
24K ALA* 3.5 22.0 - - + -
36K PHE* 3.9 16.4 - + - -
37K ASP* 3.6 1.6 - - - -
38K SER* 2.8 35.7 + - - -
67K PHE* 4.1 6.7 - + - -
70K ASN* 3.6 25.1 - - + -
71K THR* 3.8 31.6 - - + +
74K TYR* 3.6 47.8 - + + -
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Residues in contact with ILE 23 (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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8K PHE 3.6 0.9 - - - +
9K TYR* 3.3 5.4 - - - +
10K THR* 2.7 48.5 + - - +
12K MET* 4.0 11.0 - - - -
21K ARG* 3.2 40.4 - - + +
22K PHE* 1.3 83.5 - - - +
24K ALA* 1.3 64.2 + - - +
25K VAL* 4.3 12.8 - - + -
36K PHE 3.4 10.1 - - - +
37K ASP* 3.9 9.6 - - + +
53L ASP* 5.0 5.6 - - - +
54L LEU* 3.8 46.0 - - + +
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Residues in contact with ALA 24 (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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7K TYR* 5.6 0.2 - - + -
8K PHE 3.3 3.8 - - - -
9K TYR* 3.6 20.2 - - + -
22K PHE* 3.5 23.3 - - + -
23K ILE* 1.3 73.8 - - - +
25K VAL* 1.3 64.3 + - - +
34K VAL 4.5 0.3 - - - -
35K ARG* 3.3 2.9 - - - -
36K PHE* 2.7 41.9 + - + +
67K PHE* 4.0 20.7 - - + -
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Residues in contact with VAL 25 (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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7K TYR* 3.4 7.5 - - - -
8K PHE* 2.8 47.1 + - + +
23K ILE* 4.3 12.1 - - + -
24K ALA* 1.3 77.9 - - - +
26K GLY* 1.3 59.0 + - - +
27K TYR* 3.6 15.0 - - + -
32K GLN* 3.5 28.9 - - - +
34K VAL 3.4 3.8 - - - -
35K ARG* 4.2 1.8 - - + -
53L ASP* 3.6 21.1 - - + +
54L LEU 4.9 4.5 - - - +
55L SER* 3.4 27.1 - - - +
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Residues in contact with GLY 26 (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 3.4 7.2 - - - -
7K TYR* 3.6 14.6 - - - -
25K VAL* 1.3 74.5 - - - +
27K TYR* 1.3 63.7 + - - -
32K GLN* 3.3 8.0 - - - +
33K PHE* 3.2 29.3 + - - -
34K VAL* 3.0 22.2 + - - +
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Residues in contact with TYR 27 (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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5K MET* 3.3 10.2 - - - +
6K ARG* 2.7 45.4 + - + +
8K PHE* 3.8 22.0 - + + -
25K VAL* 3.6 23.8 - - + -
26K GLY* 1.3 79.6 - - - -
28K VAL* 1.3 62.4 + - - +
29K ASP 4.0 10.5 - - - +
30K ASP* 3.6 21.8 - - - -
31K THR 3.3 6.3 - - - -
32K GLN* 3.0 48.5 + - + +
33K PHE* 3.3 3.0 - - - -
55L SER* 4.0 12.9 - - - -
63L TYR* 3.7 21.4 + - - -
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Residues in contact with VAL 28 (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 3.4 3.1 - - - +
5K MET* 4.6 1.8 - - + -
27K TYR* 1.3 76.5 - - - +
29K ASP* 1.3 79.5 + - - +
30K ASP 3.0 0.9 + - - -
31K THR* 2.8 32.3 + - - -
33K PHE* 3.8 10.5 - - + -
51K TRP* 3.4 33.4 - - + -
168K LEU* 3.9 23.1 - - + -
171K TYR* 4.1 17.3 - - + -
172K LEU* 4.1 7.9 - - + -
179K LEU* 3.6 18.6 - - + +
209K TYR* 3.3 3.5 + - - -
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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