Contacts of the strand formed by residues 318 - 326 (chain A) in PDB entry 1NTZ
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 GLY 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A PHE* 4.6 2.8 - - - -
236A PHE* 4.7 0.3 - - - -
258A GLU* 3.4 9.5 - - - +
259A GLY* 2.6 34.5 + - - -
260A PRO 4.4 1.1 - - - -
312A ILE 3.2 15.3 - - - -
314A TYR* 4.4 8.5 - - - -
317A THR* 1.3 83.3 + - - +
319A LEU* 1.3 64.5 + - - +
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Residues in contact with LEU 319 (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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153A LEU* 3.7 26.9 - - + -
154A HIS* 3.8 33.7 - - + +
157A ALA* 3.8 13.9 - - + -
158A PHE* 4.0 17.3 - - + -
236A PHE* 3.7 29.2 - - + -
256A ALA* 4.0 17.0 - - + -
257A VAL 3.6 0.9 - - - -
310A PHE* 3.6 10.6 - - + -
311A ASN* 3.5 2.6 - - - +
312A ILE* 2.8 45.8 + - + +
314A TYR* 5.0 1.8 - - + -
318A GLY* 1.3 74.4 - - - +
320A LEU* 1.3 61.8 + - - +
421A ALA* 5.0 0.4 - - + -
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Residues in contact with LEU 320 (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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256A ALA* 3.2 3.1 - - - +
257A VAL* 2.9 48.6 + - + +
259A GLY* 4.5 8.1 - - - -
270A LEU* 3.5 40.2 - - + -
274A ASN* 3.5 34.3 - - - +
310A PHE 3.5 5.8 - - - +
311A ASN* 3.6 20.4 - - + +
319A LEU* 1.3 76.8 - - - +
321A GLY* 1.3 57.4 + - - +
414A TYR* 4.1 8.1 - - + -
415A PHE* 3.5 24.9 - - + -
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Residues in contact with GLY 321 (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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255A ILE 3.3 11.0 - - - -
274A ASN* 4.7 2.3 + - - +
309A THR* 3.3 5.9 - - - -
310A PHE* 2.7 50.1 + - - +
320A LEU* 1.3 78.0 - - - +
322A ALA* 1.3 56.2 + - - -
342A TRP* 3.8 17.7 - - - -
415A PHE* 4.8 1.1 - - - -
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Residues in contact with ALA 322 (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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254A ALA* 3.6 0.2 - - - -
255A ILE* 3.0 35.3 + - - +
307A PHE* 5.6 3.6 - - + -
308A GLN 3.3 13.9 - - - +
309A THR* 4.0 10.8 - - + -
310A PHE* 3.4 7.9 - - - -
321A GLY* 1.3 75.4 - - - +
323A HIS* 1.3 62.9 + - - +
324A PHE* 5.5 1.6 - - + -
338A LEU* 3.8 35.9 - - + -
342A TRP* 4.0 4.2 - - + +
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Residues in contact with HIS 323 (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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146A ARG* 4.0 13.7 + - + +
149A VAL* 5.1 2.1 - - + +
150A PHE* 3.6 34.8 - + + -
252A HIS* 3.1 35.0 + + + +
253A VAL 3.2 24.0 + - - +
254A ALA* 4.3 4.0 - - + +
306A SER* 5.1 2.4 + - - -
307A PHE* 3.2 4.0 - - - +
308A GLN* 2.9 64.0 + - + +
310A PHE* 4.0 2.2 - - + -
322A ALA* 1.3 75.3 - - - +
324A PHE* 1.3 72.0 + - - +
325A VAL* 3.7 12.9 - - + +
43I LEU* 4.9 2.8 - - - +
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Residues in contact with PHE 324 (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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251A ALA 5.2 0.2 - - - -
252A HIS* 3.5 4.3 - - - -
253A VAL* 2.9 71.0 + - + +
255A ILE* 5.3 1.3 - - + -
304A CYS* 5.0 0.4 - - + -
306A SER 3.4 13.7 - - - +
307A PHE* 3.6 11.0 - - + +
322A ALA* 5.5 1.3 - - + -
323A HIS* 1.3 82.2 - - - +
325A VAL* 1.3 68.4 + - - +
326A CYS* 3.7 24.5 - - + -
331A ILE* 4.2 13.0 - - + -
334A MET* 3.6 41.5 - - + -
335A MET* 4.4 18.6 - - - -
338A LEU* 4.6 18.4 - - + -
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Residues in contact with VAL 325 (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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250A LEU* 3.9 29.2 - - + -
251A ALA 3.2 4.5 - - - +
252A HIS* 3.3 42.4 - - + +
304A CYS* 3.5 2.4 - - - +
305A GLN* 2.8 32.0 + - + -
306A SER* 3.0 19.8 + - - +
323A HIS* 3.7 6.5 - - - +
324A PHE* 1.3 79.8 - - - +
326A CYS* 1.3 65.7 + - - +
43I LEU* 3.4 24.9 - - + -
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Residues in contact with CYS 326 (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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250A LEU* 3.5 11.9 - - - -
251A ALA* 2.7 41.0 + - - -
303A LEU 3.6 22.0 - - - +
304A CYS* 3.8 8.3 - - + +
305A GLN* 4.4 2.2 - - - +
324A PHE* 3.7 27.4 - - + -
325A VAL* 1.3 77.3 - - - +
327A ASP* 1.3 74.0 + - - +
330A SER* 4.0 3.6 - - - -
331A ILE* 3.8 23.8 - - - -
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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