Contacts of the strand formed by residues 318 - 322 (chain B) in PDB entry 3NX4
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 318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 3.0 26.5 + - - -
39B LEU 3.3 23.8 + - - -
40B ASN* 3.5 14.3 + - - +
122B MSE 3.0 20.2 + - - -
123B ILE* 2.6 37.2 + - + +
124B ILE 3.1 16.1 + - - -
125B GLY* 3.4 5.1 - - - -
127B ALA* 3.7 14.2 - - - +
158B GLY* 3.5 30.6 - - - +
161B SER* 5.6 0.7 - - - -
162B THR* 4.6 6.1 - - - +
290B PHE* 4.9 2.7 - - + -
294B ALA* 2.7 21.7 + - + +
295B ALA* 3.4 2.1 - - - -
296B THR* 3.0 27.9 + - - -
316B GLN 3.8 1.2 + - - +
317B GLY* 1.3 76.8 - - - -
319B THR* 1.3 65.2 + - - +
320B LEU 3.8 0.4 + - - -
330B NAP 5.3 1.0 + - - -
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Residues in contact with THR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 3.2 8.3 - - - -
39B LEU* 2.9 52.2 + - + +
123B ILE* 6.1 0.2 - - - -
296B THR* 3.7 10.3 - - - +
298B ILE* 3.7 37.5 - - + -
306B PHE* 4.5 13.2 - - + -
310B ILE* 3.9 16.3 - - - +
315B VAL* 4.9 8.5 - - - +
317B GLY 4.3 0.9 + - - -
318B ARG* 1.3 78.5 + - - +
320B LEU* 1.3 58.9 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 3.8 28.0 - - + -
37B SER 3.6 8.5 - - - +
38B SER* 4.4 1.8 - - - +
119B ARG* 3.6 52.3 - - + +
122B MSE 3.5 31.4 - - + -
123B ILE* 4.0 22.2 - - + +
295B ALA* 4.9 4.0 - - + -
296B THR 2.9 13.2 + - - +
297B GLU* 3.3 8.5 - - + +
298B ILE* 2.8 28.9 + - - +
318B ARG 3.8 1.4 + - - +
319B THR* 1.3 72.9 - - - +
321B VAL* 1.3 59.6 + - - +
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TRP* 3.5 6.5 - - - -
37B SER* 2.9 44.0 + - - +
38B SER* 4.0 11.2 - - - -
39B LEU* 3.9 26.5 - - + +
98B LEU* 4.0 14.4 - - + -
298B ILE* 3.6 17.0 - - + -
299B THR 4.1 4.5 - - - +
300B LEU* 4.0 20.4 - - - +
303B ALA* 5.1 1.6 - - + -
319B THR 4.5 0.4 - - - +
320B LEU* 1.3 75.5 - - - +
322B LYS* 1.3 66.6 + - - +
323B ILE* 3.4 22.9 + - + -
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B HIS 4.6 0.7 - - - +
36B TRP* 3.6 26.9 - - + -
297B GLU* 3.5 25.7 - - - +
298B ILE 2.8 17.1 + - - +
299B THR* 4.0 7.6 - - + -
300B LEU* 3.8 20.6 + - - +
320B LEU 4.0 1.4 + - - -
321B VAL* 1.3 72.7 - - - +
323B ILE* 1.3 61.3 + - - +
324B LYS* 2.9 57.0 + - + +
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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