Contacts of the strand formed by residues 33 - 38 (chain O) in PDB entry 1NJI
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 33 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3006B C 2.7 33.5 + - - -
3007B G 3.1 20.8 + - - -
23O ARG* 3.8 8.3 - - - +
26O LEU* 4.0 31.2 - - + +
27O LEU* 4.2 19.3 - - + +
31O LYS 3.7 5.8 + - - +
32O PRO* 1.3 74.8 - - - +
34O LEU* 1.3 60.3 + - - +
35O VAL* 3.5 9.9 + - + +
46O GLN 3.3 1.0 - - - +
47O LEU* 3.1 9.1 - - - +
48O VAL* 2.8 47.1 + - - +
50O LEU* 5.8 0.2 - - - +
55O ASP* 3.0 22.8 + - - -
101O VAL* 3.4 9.9 - - + +
103O ASP* 2.5 44.6 + - + -
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Residues in contact with LEU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O PRO 4.0 0.4 + - - -
33O ARG* 1.3 69.6 - - - +
35O VAL* 1.3 61.6 + - - +
36O ALA 3.2 2.3 + - - -
45O ALA* 4.7 16.8 - - + -
46O GLN 3.9 6.7 - - - +
47O LEU* 3.3 25.6 - - + -
88O ALA* 5.4 5.2 - - + -
89O GLY 6.0 0.4 - - - +
100O ALA* 4.2 7.2 - - + +
101O VAL 2.8 15.2 + - - +
102O LEU* 3.4 16.9 - - + +
103O ASP 3.0 19.9 + - - +
118O ILE* 4.5 7.4 - - + +
119O GLN* 4.2 17.0 - - + -
122O ALA* 3.4 23.3 - - + -
127O LEU* 5.1 0.7 - - + -
129O ILE* 3.4 27.4 - - + -
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Residues in contact with VAL 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3006B C 3.7 18.6 - - - -
33O ARG* 4.1 28.3 - - + +
34O LEU* 1.3 69.8 - - - +
36O ALA* 1.3 59.5 + - - +
37O ARG* 3.7 36.3 + - + +
44O ARG* 3.7 1.0 - - - +
45O ALA* 3.3 8.0 - - - -
46O GLN* 2.7 43.1 + - + +
48O VAL* 3.6 28.5 - - + -
103O ASP* 3.6 6.1 - - + -
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Residues in contact with ALA 36 (chain O).
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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34O LEU 3.2 1.2 + - - +
35O VAL* 1.3 70.5 - - - +
37O ARG* 1.3 73.6 + - - +
44O ARG 3.8 4.5 - - - -
102O LEU* 3.9 24.2 - - + -
103O ASP 3.0 13.5 + - - +
104O ILE* 4.0 3.9 - - - -
107O ASN* 3.9 9.0 - - - +
115O VAL* 4.0 18.2 - - + +
118O ILE* 3.7 28.7 - - + -
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Residues in contact with ARG 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3005B G 3.7 25.4 - - - +
3006B C 2.2 64.4 + - - -
3007B G 4.6 5.5 + - - -
17O ARG 5.2 1.9 + - - -
35O VAL* 3.7 18.4 + - + +
36O ALA* 1.3 86.2 + - - +
38O LYS* 1.3 66.8 + - - +
43O VAL* 3.6 5.0 - - - +
44O ARG* 2.8 43.4 + - + +
103O ASP* 3.1 32.3 + - - -
104O ILE 4.0 0.2 - - - -
105O GLY* 3.1 23.5 - - - +
106O LEU 5.1 1.1 - - - +
107O ASN* 4.3 1.6 - - - -
118O ILE* 4.3 1.3 - - - +
8507O CL 3.4 21.5 - - + -
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Residues in contact with LYS 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3005B G 6.0 2.3 - - - +
3028B U 4.2 4.2 + - - -
3047B A 4.3 12.5 + - - -
3048B C 2.6 29.2 + - - +
146F LYS* 3.8 10.3 + - - +
37O ARG* 1.3 82.1 - - - +
39O SER* 1.3 66.4 + - - +
42O HIS 3.6 6.7 - - - +
43O VAL* 4.0 13.0 - - + +
44O ARG 5.6 0.2 - - - -
107O ASN* 3.2 29.9 - - - +
114O LYS* 3.7 34.1 - - + +
115O VAL* 4.6 15.9 - - + -
118O ILE* 5.3 1.6 - - + -
8507O CL 3.3 16.5 - - - +
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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