Contacts of the strand formed by residues 249 - 258 (chain A) in PDB entry 3NIA
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 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LYS* 3.2 3.1 - - - -
246A ALA 2.9 34.5 + - - +
247A GLN* 3.1 16.1 + - - +
248A GLU* 1.3 83.2 - - - +
250A ASP* 1.3 64.1 + - - +
251A TYR* 3.3 31.4 + - + -
285A THR* 3.8 29.3 + - - -
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Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASP* 4.3 0.3 - - - +
46A PRO* 3.3 35.0 - - + +
190A TYR* 3.6 32.9 + - + +
243A PHE* 6.2 0.2 - - - -
244A PHE 3.6 2.2 - - - -
245A LYS* 2.7 44.4 + - - +
248A GLU 4.3 1.0 + - - +
249A ARG* 1.3 75.3 - - - +
251A TYR* 1.3 69.7 + - - +
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Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 3.9 19.7 - - + -
44A VAL 3.5 7.4 - - - +
45A ASP* 4.9 3.1 - - + +
51A VAL* 4.1 22.2 - - + -
190A TYR* 3.3 12.0 + - - -
243A PHE* 3.2 4.5 - - - -
244A PHE* 2.9 71.3 + + + +
246A ALA* 4.2 7.7 + - + -
247A GLN* 5.4 1.7 + - - -
249A ARG* 3.3 56.3 + - + +
250A ASP* 1.3 80.5 - - - +
252A ALA* 1.3 60.0 + - - +
282A ILE* 3.8 29.4 - - + +
285A THR* 4.5 5.0 + - - -
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA 3.9 0.2 - - - +
43A ILE* 3.4 5.2 - - - +
44A VAL* 3.0 42.5 + - + +
182A ALA* 3.5 24.6 - - - +
185A VAL* 3.7 17.9 - - + -
186A ALA* 3.7 13.5 - - + +
190A TYR* 4.3 5.7 - - + -
242A GLY 3.5 4.7 - - - -
243A PHE* 4.4 0.2 - - - +
251A TYR* 1.3 73.9 - - - +
253A VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 4.9 0.2 - - + -
42A ALA 3.3 10.8 - - - +
43A ILE* 4.1 14.4 - - + -
182A ALA* 4.4 3.6 - - - +
185A VAL* 4.7 2.5 - - - +
216A LEU* 4.1 16.6 - - + -
220A PHE* 5.0 1.1 - - + -
226A VAL* 6.3 0.4 - - + -
228A GLU* 6.3 0.2 - - + -
241A ILE* 3.4 2.3 - - - +
242A GLY* 2.9 51.9 + - - +
243A PHE 4.3 0.4 - - - +
244A PHE* 4.0 30.1 - - + -
252A ALA* 1.3 75.7 - - - +
254A ALA* 1.3 64.8 - - - +
255A VAL* 4.0 21.8 - - + -
278A ILE* 4.1 11.2 - - + -
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 3.7 0.9 - - - +
41A VAL* 3.4 4.5 - - - +
42A ALA 2.9 30.9 + - - +
178A PRO* 3.5 25.9 - - + +
181A MET* 4.0 2.9 - - + -
182A ALA* 3.8 13.4 - - + +
240A ASP 4.0 0.4 - - - -
241A ILE* 3.8 18.6 - - + -
253A VAL* 1.3 76.0 - - - +
255A VAL* 1.3 63.6 + - - +
256A TYR* 4.0 13.0 - - + -
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 3.3 7.2 - - - +
41A VAL* 4.3 5.6 - - + -
216A LEU* 4.0 23.8 - - + -
239A ASN* 3.3 5.0 - - - +
240A ASP* 2.8 43.5 + - + +
241A ILE* 4.2 0.6 - - - +
253A VAL* 4.0 7.6 - - + -
254A ALA* 1.3 79.0 - - - +
256A TYR* 1.3 64.5 + - - +
257A THR* 3.9 21.5 - - + -
271A VAL* 4.4 15.3 - - + -
274A VAL* 4.1 18.4 - - + -
278A ILE* 4.0 19.1 - - + -
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Residues in contact with TYR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLY 2.7 37.0 + - - +
60A PHE* 3.4 34.8 - - + -
61A ALA 3.5 17.7 - - - -
62A MET* 3.8 4.0 - - - -
65A THR* 2.8 28.7 + - - -
176A THR* 3.5 23.5 - - + +
178A PRO* 4.3 18.4 - - + -
181A MET* 3.4 16.4 - - + +
239A ASN* 3.1 33.0 - - + +
241A ILE* 3.4 26.8 - - + +
254A ALA* 4.0 11.0 - - + -
255A VAL* 1.3 75.9 - - - +
257A THR* 1.3 65.3 + - - +
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Residues in contact with THR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN 3.3 8.3 - - - -
39A ILE* 4.3 17.9 - - + -
60A PHE* 4.6 0.8 - - - -
236A GLY 5.0 0.7 + - - -
237A GLY* 3.3 3.5 - - - -
238A ARG* 2.7 57.0 + - - +
239A ASN* 3.2 3.8 + - - +
255A VAL* 3.9 18.6 - - + -
256A TYR* 1.3 79.8 - - - +
258A THR* 1.3 68.7 + - - +
259A ALA* 5.2 0.5 + - - +
267A ARG* 5.6 0.9 - - - +
270A LEU* 3.9 22.7 - - + +
271A VAL* 4.0 11.1 - - + +
274A VAL* 4.7 4.5 - - + -
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Residues in contact with THR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ALA* 3.2 4.6 - - - -
38A GLN* 2.9 50.8 + - - +
60A PHE* 3.8 18.0 - - - -
167A ASN* 4.4 15.1 + - - +
235A ASN* 3.5 24.5 - - + +
236A GLY 3.4 4.3 - - - +
237A GLY* 4.7 0.7 - - - -
257A THR* 1.3 78.6 + - - +
259A ALA* 1.3 60.8 + - - +
260A PRO* 3.9 11.9 - - + +
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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