Contacts of the helix formed by residues 295 - 312 (chain A) in PDB entry 1NBF
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 ASP 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TYR* 4.8 0.7 - - - -
294A HIS* 1.3 77.1 - - - +
296A VAL* 1.3 58.0 + - - +
297A GLN* 2.7 34.8 + - - +
298A GLU* 2.9 20.4 + - + +
299A LEU* 3.2 24.8 + - - +
514A TYR* 2.6 29.8 + - - -
342D ARG* 3.5 10.0 + - - -
372D ARG* 3.6 25.1 - - + +
373D LEU 3.1 28.3 + - - +
374D ARG* 4.0 3.0 - - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TYR* 3.2 29.4 - - - +
227A SER* 4.7 2.9 - - - -
228A LEU* 3.9 15.3 - - + +
294A HIS 3.7 2.2 + - - -
295A ASP* 1.3 70.5 + - - +
297A GLN* 1.3 66.7 + - - +
299A LEU* 3.4 6.0 + - + +
300A CYS* 3.0 25.8 + - - +
454A LEU* 3.9 34.3 - - + -
465A TYR* 3.3 36.3 + - + +
514A TYR* 4.2 9.0 - - + -
515A MET* 4.5 7.3 - - - +
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP* 2.7 14.0 + - - +
296A VAL* 1.3 75.5 - - - +
298A GLU* 1.3 57.1 + - - +
300A CYS* 3.3 3.2 + - - +
301A ARG* 3.0 37.0 + - - +
349A ASP* 2.7 29.7 + - - +
405A GLN* 3.4 27.2 - - + +
514A TYR* 4.2 13.2 - - + +
515A MET* 4.2 22.7 - - + -
342D ARG* 2.7 40.1 + - - -
344D ILE* 3.2 24.6 - - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A HIS* 5.2 10.2 - - - -
295A ASP* 2.9 23.2 + - - +
297A GLN* 1.3 76.5 + - - +
299A LEU* 1.3 65.3 + - - +
301A ARG* 3.3 2.8 + - - +
302A VAL* 3.1 29.3 + - + +
342D ARG* 3.4 22.7 - - - +
349D GLN* 3.0 27.7 + - - +
372D ARG* 2.8 48.7 + - - +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TYR* 3.9 22.4 - - + +
225A MET* 3.7 37.5 - - + -
228A LEU* 3.8 22.7 - - + -
283A PHE* 5.0 12.3 - - + -
285A TRP* 6.2 2.2 - - + -
294A HIS* 5.9 0.2 - - + -
295A ASP 3.2 10.6 + - - +
296A VAL 3.6 8.1 - - - +
297A GLN 3.3 0.2 - - - -
298A GLU* 1.3 78.4 - - - +
300A CYS* 1.3 58.2 + - - +
302A VAL* 4.7 6.7 - - + -
303A LEU* 2.8 52.8 + - + +
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Residues in contact with CYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.0 27.3 - - + +
232A LEU* 5.0 1.1 - - - -
296A VAL 3.0 14.9 + - - +
297A GLN* 3.5 12.1 - - - +
298A GLU 3.2 0.2 - - - -
299A LEU* 1.3 78.0 - - - +
301A ARG* 1.3 71.2 + - - +
303A LEU* 4.6 0.7 - - - -
304A LEU* 3.0 55.2 + - - +
403A HIS* 3.8 26.0 - - - -
515A MET* 4.5 6.3 - - + -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLN* 3.0 37.9 + - - +
298A GLU* 3.7 7.9 - - - +
300A CYS* 1.3 85.2 - - - +
302A VAL* 1.3 63.0 + - - +
304A LEU* 3.8 28.0 - - - +
305A ASP* 3.3 24.6 + - - +
348A TYR* 3.3 31.8 + - - +
349A ASP* 2.9 30.5 + - - +
403A HIS* 5.1 2.2 + - - +
515A MET* 6.2 0.4 - - - -
342D ARG* 5.0 0.4 - - - +
344D ILE* 4.0 18.8 - - + -
347D GLY* 2.8 35.8 + - - +
348D LYS* 4.5 2.0 - - - +
349D GLN* 4.3 22.2 - - + +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLU* 3.1 27.4 + - + +
299A LEU* 4.1 7.2 - - + +
301A ARG* 1.3 76.9 - - - +
303A LEU* 1.3 57.6 + - - +
305A ASP* 3.5 6.2 + - - +
306A ASN* 3.1 28.3 + - + +
349D GLN* 4.7 19.5 - - + +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 6.2 1.1 - - + -
228A LEU* 3.8 25.4 - - + -
229A LEU* 5.0 13.0 - - + -
232A LEU* 4.5 10.3 - - + -
256A VAL* 4.4 16.4 - - + -
260A LEU* 4.7 11.0 - - + -
279A LEU* 5.9 1.1 - - + -
283A PHE* 4.5 18.2 - - + -
299A LEU* 2.8 37.7 + - + +
300A CYS 4.1 1.1 - - - +
302A VAL* 1.3 74.6 - - - +
304A LEU* 1.3 62.7 + - + +
306A ASN* 3.2 7.5 + - - +
307A VAL* 2.8 51.7 + - + +
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.3 24.9 - - + -
238A LEU* 4.7 4.3 - - + -
300A CYS* 3.0 40.1 + - - +
301A ARG* 3.8 18.6 - - - +
303A LEU* 1.3 78.2 - - + +
305A ASP* 1.3 56.8 + - - +
307A VAL* 4.6 3.6 - - + -
308A GLU* 2.8 31.6 + - - +
320A ILE* 3.5 25.5 - - + +
324A PHE* 4.0 42.0 - - + -
348A TYR* 5.0 4.7 - - + -
403A HIS* 4.6 3.8 - - + +
348D LYS* 5.3 0.2 - - - -
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG 3.3 18.4 + - - +
302A VAL* 3.7 6.2 - - - +
303A LEU 3.2 0.4 - - - -
304A LEU* 1.3 79.8 - - - +
306A ASN* 1.3 58.9 + - - +
308A GLU* 3.3 1.8 + - - +
309A ASN* 2.9 48.1 + - - +
348D LYS* 2.8 49.7 + - + +
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 3.8 38.0 - - - +
283A PHE* 5.2 3.2 - - - -
302A VAL* 3.1 17.7 + - + +
303A LEU* 3.5 11.0 - - - +
305A ASP* 1.3 82.1 - - - +
307A VAL* 1.3 61.6 + - - +
309A ASN* 3.3 7.9 + - - +
310A LYS* 3.0 36.3 + - - +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 5.6 0.7 - - + -
242A VAL* 4.7 10.8 - - + -
245A MET* 4.4 10.8 - - + -
256A VAL* 4.7 7.9 - - + -
257A PRO* 6.0 3.6 - - + -
260A LEU* 3.7 26.9 - - + -
303A LEU* 2.8 34.9 + - + +
304A LEU* 4.5 3.6 - - + -
306A ASN* 1.3 72.1 - - - +
308A GLU* 1.3 63.0 + - - +
310A LYS* 3.3 7.3 + - - +
311A MET* 3.0 38.9 + - + +
320A ILE* 3.7 19.1 - - + -
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Residues in contact with GLU 308 (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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304A LEU 2.8 18.9 + - - +
305A ASP 3.5 5.4 - - - +
306A ASN 3.2 0.2 - - - -
307A VAL* 1.3 76.6 - - - +
309A ASN* 1.3 64.5 + - - +
311A MET* 3.1 15.3 + - - +
312A LYS* 3.2 34.0 + - + +
318A GLY 5.6 4.1 + - - +
320A ILE* 3.5 14.2 - - + +
321A PRO* 3.3 31.0 - - + +
325A ARG* 5.1 1.7 + - - -
348A TYR* 2.8 32.4 + - - -
348D LYS* 3.1 19.4 + - - -
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 2.9 41.6 + - - +
306A ASN* 3.3 5.9 + - - +
308A GLU* 1.3 77.4 - - - +
310A LYS* 1.3 64.0 + - + +
312A LYS* 3.0 48.2 + - - +
360C ASN* 3.3 22.3 - - - +
362C GLN* 3.2 14.0 + - - -
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Residues in contact with LYS 310 (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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245A MET* 3.8 19.6 - - + +
254A LYS 5.9 1.7 + - - -
255A SER* 6.4 0.4 - - - +
256A VAL* 6.0 2.5 - - - +
257A PRO* 4.0 25.8 - - + +
306A ASN* 3.0 34.5 + - - +
307A VAL* 3.7 7.2 - - - +
309A ASN* 1.3 78.4 - - + +
311A MET* 1.3 59.0 - - - +
312A LYS 3.6 2.8 + - - +
314A THR* 3.9 11.3 - - - +
343B ARG* 5.6 0.2 + - - -
362C GLN* 4.2 19.1 + - - +
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Residues in contact with MET 311 (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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238A LEU* 4.8 2.9 - - + -
241A ALA* 3.7 42.6 - - + +
242A VAL* 3.9 11.0 - - + +
245A MET* 3.4 29.6 - - + -
307A VAL* 3.0 23.1 + - + +
308A GLU* 3.5 7.2 - - + +
309A ASN 3.1 0.8 - - - -
310A LYS* 1.3 75.6 - - - +
312A LYS* 1.3 63.4 + - - +
314A THR* 2.7 28.0 + - - +
316A VAL* 3.7 25.1 - - + +
317A GLU* 3.2 12.6 - - - -
318A GLY 4.9 1.6 - - - +
319A THR* 4.0 11.7 - - + -
320A ILE* 4.3 15.0 - - - -
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Residues in contact with LYS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 3.2 32.1 + - + +
309A ASN* 3.0 31.0 + - - +
310A LYS 3.9 4.0 - - - +
311A MET* 1.3 78.5 - - - +
313A GLY* 1.3 59.1 + - - +
314A THR* 3.6 0.5 + - - +
317A GLU* 3.8 18.4 - - + +
318A GLY 5.7 1.3 - - - +
343B ARG* 3.5 19.1 + - - -
360C ASN* 3.3 20.0 + - + +
362C GLN* 3.6 10.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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