Contacts of the helix formed by residues 292 - 308 (chain A) in PDB entry 1N3C
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 SER 292 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLN* 3.9 3.8 + - - -
288A ALA* 4.1 7.9 - - - -
290A GLY 4.0 4.5 - - - -
291A PRO* 1.3 74.6 - - - +
293A PRO* 1.3 77.3 - - - +
294A GLN* 3.1 10.2 + - - +
295A THR* 2.7 31.3 + - - +
296A ASN* 2.9 27.3 + - - +
3B T 3.8 16.9 + - - -
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Residues in contact with PRO 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 5.9 2.7 - - - +
292A SER* 1.3 88.8 - - - +
294A GLN* 1.3 60.2 + - + +
296A ASN* 3.8 7.0 - - + +
297A LYS* 3.2 21.5 + - - +
2B G 5.7 3.1 - - + -
3B T 5.0 19.3 - - + +
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER* 4.4 6.9 - - - -
287A GLN* 2.9 32.5 - - - +
292A SER* 3.1 5.8 + - - +
293A PRO* 1.3 82.4 - - + +
295A THR* 1.3 61.1 + - - +
297A LYS* 3.6 5.9 + - - +
298A GLU* 3.4 20.3 + - - +
2B G 5.4 3.8 - - - -
3B T 5.7 0.2 - - - +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TRP* 3.1 17.5 - - - -
281A TRP* 3.9 3.3 - - - -
283A PRO* 4.0 8.5 - - + -
286A SER* 3.7 23.6 - - - -
287A GLN* 4.4 0.2 - - - +
288A ALA* 3.9 19.3 - - + +
290A GLY 2.9 18.3 + - - +
292A SER* 2.7 38.2 + - - +
294A GLN* 1.3 73.3 - - - +
296A ASN* 1.3 66.3 + - - +
298A GLU* 3.1 7.4 + - - +
299A LEU* 2.9 22.3 + - - +
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Residues in contact with ASN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A THR* 6.2 4.9 - - + -
267A VAL* 3.7 34.7 - - + +
268A ASN* 5.9 0.6 - - - -
272A TRP* 3.1 24.4 - - - +
291A PRO* 3.6 6.7 - - - +
292A SER 2.9 26.4 + - - +
293A PRO* 3.8 5.9 - - + +
295A THR* 1.3 82.6 + - - +
297A LYS* 1.3 62.4 - - - +
299A LEU* 3.1 4.9 + - - +
300A GLY* 2.9 19.4 + - - -
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Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A HIS* 5.4 6.9 + - - -
248A THR* 5.3 17.0 - - - +
293A PRO 3.2 14.0 + - - +
294A GLN* 3.8 7.0 - - - +
295A THR 3.3 0.2 - - - -
296A ASN* 1.3 77.9 - - - +
298A GLU* 1.3 64.8 + - - +
300A GLY* 3.2 3.6 + - - +
301A ASN* 2.9 38.4 + - - +
304A ARG* 4.8 4.5 + - - +
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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
----------------------------------------------------------
281A TRP* 3.9 10.8 - - + -
283A PRO* 3.7 7.0 - - - +
284A THR* 2.7 36.8 + - - +
285A THR* 2.9 25.1 + - - +
286A SER* 3.1 30.5 - - - -
294A GLN 3.4 7.8 + - - +
295A THR 3.1 9.3 + - - +
297A LYS* 1.3 79.1 - - - +
299A LEU* 1.3 56.7 + - - +
301A ASN* 3.0 11.0 + - + +
302A PHE* 2.8 29.4 + - + +
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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
----------------------------------------------------------
267A VAL* 3.6 24.9 - - + -
271A MET* 4.0 18.8 - - + +
272A TRP* 3.8 20.0 - - + +
275A ALA* 3.7 13.5 - - + -
281A TRP* 3.7 26.8 - - + -
295A THR 2.9 13.3 + - - +
296A ASN* 3.4 9.4 - - - +
298A GLU* 1.3 74.7 - - - +
300A GLY* 1.3 62.6 - - - +
302A PHE* 3.1 14.3 + - + +
303A PHE* 3.0 49.1 + - + -
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Residues in contact with GLY 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 4.0 14.8 - - - +
267A VAL* 3.7 17.2 - - - +
296A ASN 2.9 11.8 + - - -
297A LYS* 3.2 4.2 + - - -
299A LEU* 1.3 76.7 - - - +
301A ASN* 1.3 60.6 + - - +
303A PHE* 3.5 3.3 + - - +
304A ARG* 3.1 38.3 + - - +
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Residues in contact with ASN 301 (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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297A LYS* 2.9 32.1 + - - +
298A GLU* 3.0 11.1 + - - +
300A GLY* 1.3 73.2 - - - +
302A PHE* 1.3 66.2 + - - +
304A ARG* 2.7 40.6 + - - +
305A SER* 2.9 26.1 + - - -
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 4.2 30.3 - + + -
281A TRP* 3.4 43.1 - + + +
298A GLU* 2.8 13.0 + - + +
299A LEU* 3.1 16.8 + - + +
301A ASN* 1.3 76.2 - - - +
303A PHE* 1.3 86.6 + + - +
305A SER* 3.0 11.3 + - - -
306A LEU* 2.9 41.6 + - + +
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Residues in contact with PHE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A VAL* 4.0 24.0 - - + -
267A VAL* 5.3 0.4 - - + -
271A MET* 4.2 19.5 - - + -
274A ILE* 4.4 7.4 - - + -
275A ALA* 3.8 26.0 - - + -
279A TYR* 4.2 15.3 - + - -
299A LEU* 3.0 45.9 + - + +
300A GLY* 3.9 4.5 - - - +
302A PHE* 1.3 92.3 - + - +
304A ARG* 1.3 59.9 + - - +
306A LEU* 3.6 6.0 - - + +
307A TRP* 3.0 72.1 + + + +
311A ALA* 3.7 3.9 - - - +
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TYR* 4.0 23.3 + - - -
263A GLN* 2.9 50.0 + - + -
265A VAL* 3.4 26.2 + - - +
297A LYS* 4.8 5.1 + - - +
300A GLY* 3.1 24.6 + - - +
301A ASN* 2.7 39.7 + - - +
303A PHE* 1.3 76.9 - - - +
305A SER* 1.3 58.0 + - - +
308A GLY* 2.7 40.4 + - - +
311A ALA* 3.7 6.7 - - - +
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Residues in contact with SER 305 (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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301A ASN 2.9 12.4 + - - -
302A PHE* 3.0 19.6 + - - -
304A ARG* 1.3 76.5 - - - +
306A LEU* 1.3 60.3 + - - +
308A GLY* 4.5 1.6 + - - -
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Residues in contact with LEU 306 (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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116A VAL* 3.6 35.9 - - + +
117A ASP* 3.5 29.8 - - + +
279A TYR* 3.6 23.3 - - + -
302A PHE* 2.9 29.3 + - + +
303A PHE* 3.6 13.2 - - + +
304A ARG 3.0 0.2 - - - -
305A SER* 1.3 81.7 + - - +
307A TRP* 1.3 76.9 + - + +
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Residues in contact with TRP 307 (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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112A HIS* 3.5 24.2 + - - -
113A TRP* 3.6 31.6 + + + -
116A VAL* 4.7 2.9 - - + -
117A ASP* 3.1 26.4 + - + +
120A PHE* 4.3 7.7 - + - -
271A MET* 6.1 1.6 - - - -
274A ILE* 5.6 0.2 - - + -
279A TYR* 3.5 19.3 - - - -
303A PHE* 3.0 57.0 + + + +
306A LEU* 1.3 92.6 - - + +
308A GLY* 1.3 59.5 + - - +
309A PRO* 4.5 0.5 - - - +
310A TYR 5.0 0.2 + - - -
311A ALA* 3.4 27.4 - - - -
314A ALA* 3.4 14.8 - - + -
315A GLN* 3.7 28.5 - - + -
318A LEU* 3.6 23.8 - - + -
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Residues in contact with GLY 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS* 5.2 1.3 - - - -
263A GLN* 4.4 0.2 - - - +
304A ARG* 2.7 29.2 + - - +
305A SER 4.5 1.3 - - - -
306A LEU 3.7 0.6 - - - -
307A TRP* 1.3 73.6 - - - +
309A PRO* 1.3 66.5 - - - +
310A TYR 3.1 3.4 - - - -
311A ALA* 2.8 30.7 + - - +
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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