Contacts of the strand formed by residues 309 - 322 (chain A) in PDB entry 1NQF
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 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ILE* 3.3 13.5 - - - +
306A VAL 3.3 18.1 + - - -
307A GLY 3.2 3.0 + - - -
308A HIS* 1.3 80.3 - - - +
310A SER* 1.3 64.2 + - - -
345A LEU* 3.2 18.6 - - - -
346A GLN* 3.4 3.9 + - - -
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Residues in contact with SER 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 4.3 6.6 + - - -
17A GLN* 5.3 0.9 + - - -
303A ASN* 3.1 26.5 + - - -
304A VAL 3.1 18.2 - - - -
305A ILE* 4.5 3.1 - - - -
306A VAL* 4.2 3.6 - - - +
309A GLY* 1.3 75.4 - - - -
311A ILE* 1.3 64.9 + - - +
344A GLY* 3.6 2.0 - - - -
345A LEU* 2.8 43.4 + - - +
346A GLN* 4.2 4.7 + - - +
803A C8E 4.2 4.0 + - - -
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASN* 3.5 4.6 - - - -
304A VAL* 3.1 40.0 + - + +
306A VAL* 4.3 13.5 - - + -
310A SER* 1.3 76.8 - - - +
312A GLY* 1.3 64.2 + - - +
342A LEU* 4.5 6.1 - - + -
343A THR 3.3 10.3 - - - +
344A GLY* 5.1 0.7 - - - -
803A C8E 3.4 38.8 - - + +
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Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASN 3.3 12.1 - - - -
303A ASN* 4.1 5.2 - - - -
311A ILE* 1.3 81.7 - - - +
313A ALA* 1.3 64.1 + - - +
342A LEU* 3.1 7.1 - - - +
343A THR* 2.6 52.2 + - - +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ALA* 3.4 1.2 - - - -
302A ASN* 2.8 33.4 + - - +
312A GLY* 1.3 76.6 - - - +
314A GLY* 1.3 59.6 + - - +
341A TYR* 3.1 22.7 - - - +
342A LEU* 4.0 7.0 - - + +
343A THR* 4.5 0.2 + - - -
800A C8E 5.5 4.0 - - + -
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TRP 2.8 14.1 - - - -
301A ALA* 3.7 4.3 - - - -
313A ALA* 1.3 74.9 - - - +
315A VAL* 1.3 65.3 + - - +
340A ILE* 3.7 6.2 - - - +
341A TYR* 3.1 48.0 + - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL 4.1 0.7 - - - +
299A GLN* 3.3 4.6 - - - +
300A TRP* 2.6 53.3 + - + +
314A GLY* 1.3 78.1 - - - +
316A ASP* 1.3 60.8 + - - +
317A MSE 4.2 0.7 - - + -
338A THR* 5.1 9.9 - - + -
339A GLY 3.5 13.5 - - - +
340A ILE* 4.4 14.8 - - + -
341A TYR* 5.1 1.1 - - - -
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Residues in contact with ASP 316 (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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14A ARG* 3.4 15.5 + - - +
118A TYR* 4.2 5.4 - - - +
297A THR* 4.4 2.3 - - - +
298A VAL 4.0 0.6 - - - +
299A GLN* 2.8 34.2 + - + +
314A GLY 4.2 0.2 - - - -
315A VAL* 1.3 74.3 - - - +
317A MSE 1.3 67.3 + - - +
318A GLN* 5.8 1.7 - - - +
337A ASN* 4.0 0.7 - - - +
338A THR* 3.4 3.0 + - - -
339A GLY 2.7 41.7 + - - +
341A TYR* 5.0 2.9 - - + -
358A ARG* 3.3 36.4 + - - +
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Residues in contact with MSE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR 4.0 0.4 - - - +
297A THR* 3.4 6.6 - - - +
298A VAL* 2.9 59.2 + - + +
315A VAL* 4.2 0.6 - - + -
316A ASP* 1.3 76.0 + - - +
318A GLN* 1.3 71.5 + - - +
319A MSE 4.9 12.8 - - + +
336A ARG* 6.5 0.2 - - + -
337A ASN 3.5 4.7 - - - +
338A THR* 3.6 19.3 - - + +
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Residues in contact with GLN 318 (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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84A ARG* 3.4 50.4 + - - +
295A GLN* 3.9 23.4 - - + +
296A TYR 3.4 9.0 - - - +
297A THR* 4.0 11.7 + - + +
316A ASP* 4.4 1.8 - - - +
317A MSE 1.3 79.3 - - - +
319A MSE 1.3 67.5 + - - +
320A GLN* 4.1 14.4 + - + +
335A GLN 4.0 0.3 - - - +
336A ARG* 3.5 2.8 - - - +
337A ASN* 2.8 53.7 + - + +
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Residues in contact with MSE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLN* 3.4 3.3 - - - +
296A TYR* 2.7 66.7 + - + +
317A MSE 4.9 12.3 - - + +
318A GLN* 1.3 72.8 - - - +
320A GLN* 1.3 62.4 + - - +
321A MSE 3.6 23.6 - - + -
334A ASP* 4.2 0.4 - - - +
335A GLN 3.5 2.2 - - - +
336A ARG* 3.0 63.3 - - + +
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Residues in contact with GLN 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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84A ARG* 5.5 2.5 + - - +
88A ALA* 3.1 26.4 - - - +
293A MSE 3.5 14.1 - - + +
294A LYS 3.5 3.8 - - - -
295A GLN* 2.8 30.8 + - + +
318A GLN* 4.1 20.5 + - + +
319A MSE 1.3 76.5 - - - +
321A MSE 1.3 63.4 + - - +
322A THR* 3.9 1.8 + - - +
333A TYR 3.5 1.7 - - - +
334A ASP* 3.1 6.8 - - - +
335A GLN* 2.8 74.6 + - + +
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Residues in contact with MSE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 4.0 0.7 - - - +
293A MSE 3.3 4.5 - - - -
294A LYS* 2.7 50.7 + - + +
296A TYR* 3.1 32.8 - - + +
319A MSE 3.6 22.0 - - + -
320A GLN* 1.3 72.2 - - - +
322A THR* 1.3 61.4 + - - +
323A THR 4.1 0.2 + - - -
333A TYR 3.7 3.6 - - - -
334A ASP* 3.5 34.8 - - + +
336A ARG* 5.2 1.8 - - - +
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Residues in contact with THR 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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90A VAL* 3.7 9.2 - - + -
292A GLU 3.7 2.5 - - - +
293A MSE 3.6 32.1 - - + +
320A GLN 4.2 3.6 + - - -
321A MSE 1.3 74.6 - - - +
323A THR* 1.3 61.9 + - - +
324A PRO* 4.2 0.3 - - - +
326A THR* 3.4 30.3 - - + +
332A GLY* 3.4 3.1 - - - -
333A TYR* 2.8 37.3 + - - +
335A GLN* 4.5 2.6 + - - -
398A LEU* 3.6 23.7 - - + +
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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