Contacts of the strand formed by residues 18 - 24 (chain 4) 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 GLN 18 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84 ASN* 4.1 6.7 - - - +
94 THR 3.1 19.2 + - - -
144 CYS* 3.7 16.3 - - - +
164 GLU* 3.4 37.6 + - - +
174 HIS* 1.3 82.8 - - - +
194 GLU* 1.3 62.8 + - - +
204 HIS* 2.8 21.3 + - + -
714 CYS* 4.2 13.0 - - - -
724 GLY 5.4 0.2 - - - +
734 GLU* 2.8 48.0 + - - +
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Residues in contact with GLU 19 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64 ARG* 3.7 39.7 + - + +
74 PHE 3.6 11.0 - - - +
84 ASN* 3.7 15.1 + - - +
184 GLN* 1.3 73.5 - - - +
204 HIS* 1.3 71.4 + - - +
724 GLY* 2.8 33.7 + - - -
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Residues in contact with HIS 20 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64 ARG* 3.1 10.2 - - - +
74 PHE* 2.9 37.3 + - + +
94 THR* 3.0 35.8 + - + +
104 TYR 3.6 7.9 + - - -
114 CYS* 3.4 35.1 - - + +
184 GLN* 2.8 24.3 + - - -
194 GLU* 1.3 76.0 - - - +
214 GLU* 1.3 63.7 + - - +
224 VAL* 4.2 1.8 - - - -
694 TYR* 4.1 8.3 - - + -
704 ARG 3.0 8.5 - - - +
714 CYS* 3.4 28.3 - - + +
724 GLY 5.1 0.2 - - - -
764 LYS 5.3 0.2 + - - -
784 HIS* 3.8 24.2 + + - -
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Residues in contact with GLU 21 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 ARG* 3.4 28.5 + - + +
64 ARG* 3.5 40.2 + - + +
204 HIS* 1.3 74.1 - - - +
224 VAL* 1.3 68.4 + - - +
234 GLU* 4.0 12.2 + - - +
684 LYS 3.4 3.6 - - - +
694 TYR* 3.7 0.7 - - - -
704 ARG* 2.8 48.8 + - + +
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Residues in contact with VAL 22 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34 MET* 4.5 4.0 - - + -
44 PRO 4.2 4.5 - - - +
54 ARG* 2.7 51.2 + - - +
74 PHE* 3.3 36.6 - - + -
204 HIS 5.2 0.9 - - - +
214 GLU* 1.3 76.8 - - - +
234 GLU* 1.3 58.4 + - - +
674 LEU* 3.9 27.6 - - + -
684 LYS 3.5 7.2 - - - +
694 TYR* 3.8 16.6 - - + -
904 PHE* 3.4 25.3 - - + -
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Residues in contact with GLU 23 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 ARG* 4.0 9.0 - - - +
214 GLU* 4.0 11.9 + - - +
224 VAL* 1.3 75.4 - - - +
244 LYS* 1.3 75.4 + - - +
264 ARG* 4.2 26.8 + - + +
674 LEU* 3.4 7.7 - - - +
684 LYS* 2.8 59.9 + - + +
704 ARG* 4.4 14.5 + - - -
904 PHE* 4.6 0.4 - - - -
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Residues in contact with LYS 24 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54 ARG* 5.1 0.2 - - - +
234 GLU* 1.3 88.3 - - - +
254 VAL* 1.3 68.6 + - - +
264 ARG* 3.0 11.1 + - - +
664 ASP 3.7 7.2 - - - +
674 LEU* 3.8 10.5 - - + -
684 LYS* 5.4 0.2 - - - -
874 ARG* 6.1 0.4 - - - +
884 LEU* 3.1 35.5 + - - +
904 PHE* 3.7 25.0 - - + -
85044 CL 3.9 19.1 - - + -
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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