Contacts of the helix formed by residues 288 - 301 (chain A) in PDB entry 6C90
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 ASN 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ILE* 3.9 5.5 - - - +
287A PRO* 1.3 74.5 - - + +
289A ALA* 1.3 63.5 + - - +
290A ARG* 3.3 4.3 - - - +
291A GLN* 3.2 41.5 + - + +
292A PHE* 3.3 12.1 + - - +
558A PRO* 3.4 14.9 - - + +
559A LEU* 2.8 53.4 + - - +
589A PHE* 4.3 4.4 - - - -
593A GLN* 3.6 3.6 - - - +
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Residues in contact with ALA 289 (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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158A LEU* 3.5 23.1 - - + +
160A SER* 4.4 8.7 - - - -
286A ILE* 3.7 22.4 + - + +
287A PRO 3.5 3.0 - - - -
288A ASN* 1.3 76.2 - - - +
290A ARG* 1.3 63.3 + - - +
292A PHE* 3.1 2.8 + - - -
293A ALA* 3.1 19.8 + - - +
306A VAL* 3.6 24.2 - - + +
308A TYR* 4.8 2.2 - - + -
1108A TLA 3.7 12.4 + - - +
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Residues in contact with ARG 290 (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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101A VAL* 3.8 28.2 - - + +
113A GLU* 2.9 41.2 + - - +
115A ALA* 6.1 0.4 - - + -
288A ASN* 3.3 0.6 - - - -
289A ALA* 1.3 78.8 - - - +
291A GLN* 1.3 62.7 + - - +
293A ALA* 3.2 3.5 + - - +
294A GLU* 2.9 43.2 + - - +
306A VAL* 4.2 12.5 - - + +
1108A TLA 4.1 29.3 + - - +
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASN* 3.2 30.8 + - + +
290A ARG* 1.3 77.9 - - - +
292A PHE* 1.3 62.6 + - - +
294A GLU* 3.3 13.7 + - - +
295A TRP* 3.1 18.7 + - - +
589A PHE* 3.9 7.1 - - + -
592A PHE* 3.7 6.6 - - + -
593A GLN* 3.1 43.9 + - - +
596A ARG* 3.5 36.5 - - + +
597A ALA* 4.8 3.6 - - - +
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Residues in contact with PHE 292 (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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158A LEU* 4.1 19.5 - - + -
254A ILE* 4.2 9.4 - - + -
266A TRP* 3.3 43.1 - + - -
270A ILE* 4.3 0.4 - - + -
281A PHE* 3.7 38.8 - + - -
286A ILE* 5.3 4.5 - - + -
288A ASN* 3.3 7.8 + - - +
289A ALA* 3.1 10.5 + - - +
291A GLN* 1.3 79.6 - - - +
293A ALA* 1.3 64.0 + - - +
295A TRP* 3.1 27.5 + + - +
296A ILE* 3.0 42.1 + - + +
559A LEU* 4.9 6.5 - - + -
589A PHE* 3.9 21.9 - + + -
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Residues in contact with ALA 293 (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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115A ALA* 3.9 5.6 - - + -
158A LEU* 5.2 2.5 - - + -
289A ALA 3.1 5.8 + - - +
290A ARG* 3.7 4.0 - - - +
292A PHE* 1.3 79.3 - - - +
294A GLU* 1.3 63.5 + - - +
296A ILE* 3.3 2.6 + - - +
297A CYS* 2.9 23.9 + - - +
304A CYS* 3.7 36.3 - - - +
305A HIS 4.3 0.2 - - - +
306A VAL* 3.3 34.3 - - + -
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Residues in contact with GLU 294 (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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99A VAL* 3.8 14.0 - - + +
101A VAL* 3.7 27.7 - - + +
115A ALA* 3.8 11.6 - - + +
290A ARG* 2.9 35.2 + - - +
291A GLN* 3.5 14.8 - - - +
293A ALA* 1.3 75.8 - - - +
295A TRP* 1.3 56.8 + - - +
297A CYS* 3.2 2.3 + - - +
298A HIS* 2.8 30.1 + - - +
592A PHE* 3.6 13.0 - - + -
596A ARG* 2.8 41.2 + - - -
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Residues in contact with TRP 295 (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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266A TRP* 5.2 0.2 - + - -
267A GLU* 4.1 20.9 - - + -
270A ILE* 4.0 17.5 - - + -
271A ILE* 4.1 7.0 - - + -
291A GLN 3.1 6.5 + - - +
292A PHE* 3.1 35.3 + + - +
294A GLU* 1.3 75.7 - - - +
296A ILE* 1.3 69.0 + - + +
298A HIS* 3.1 8.7 + + - +
299A LEU* 2.7 59.6 + - + +
587A LYS 2.8 23.7 + - - -
588A SER 3.5 0.6 - - - -
589A PHE* 3.4 55.8 - + + +
592A PHE* 3.6 38.3 - + + -
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Residues in contact with ILE 296 (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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156A SER* 5.0 2.5 - - - -
270A ILE* 3.7 25.8 - - + -
279A TYR* 4.3 9.4 - - + -
281A PHE* 3.5 29.8 - - + -
292A PHE* 3.0 29.9 + - + +
293A ALA 3.3 6.5 + - - +
295A TRP* 1.3 90.9 - - + +
297A CYS* 1.3 58.7 + - - +
299A LEU* 3.2 4.3 + - + +
300A HIS* 2.9 42.2 + - + +
302A GLN 4.8 0.6 - - - +
304A CYS* 4.0 21.5 - - + -
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Residues in contact with CYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 3.9 8.7 - - + -
115A ALA* 4.0 12.3 - - + +
116A LEU* 3.2 41.3 - - - -
117A PRO* 3.3 10.0 - - - +
293A ALA 2.9 14.7 + - - +
294A GLU 3.5 8.3 - - - +
296A ILE* 1.3 77.0 - - - +
298A HIS* 1.3 56.8 + - - +
301A LYS* 2.8 32.4 + - - +
302A GLN 3.3 25.4 - - - +
304A CYS* 4.5 1.7 - - - +
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Residues in contact with HIS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 5.1 6.3 - - + -
96A MET 4.3 4.3 - - - -
97A PRO* 3.4 35.9 - - + +
98A ARG 4.6 1.2 + - - -
99A VAL* 3.9 11.3 - - + +
294A GLU 2.8 17.4 + - - +
295A TRP* 3.4 13.7 - + - +
297A CYS* 1.3 72.7 - - - +
299A LEU* 1.3 64.7 + - + +
301A LYS* 3.1 38.4 + - - +
586A GLU 4.7 8.5 + - - -
587A LYS* 3.7 38.7 + - + +
592A PHE* 3.6 31.2 - + + -
595A TYR* 5.2 3.4 - + - -
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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
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270A ILE* 3.7 23.3 - - + -
271A ILE* 4.0 22.2 - - + +
275A ASP* 4.0 5.7 - - - +
295A TRP* 2.7 59.6 + - + +
296A ILE* 3.6 6.3 - - + +
297A CYS 3.2 0.2 - - - -
298A HIS* 1.3 80.9 - - + +
300A HIS* 1.3 73.5 + - + +
301A LYS* 3.8 8.0 + - - +
583A TYR* 4.8 10.5 + - - +
587A LYS* 3.7 34.8 - - + +
659B PRO* 5.6 3.5 - - - +
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Residues in contact with HIS 300 (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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270A ILE* 2.9 28.5 + - + +
271A ILE 4.5 5.4 - - - -
273A LEU 3.3 18.3 + - - -
274A PRO 4.5 0.2 - - - -
275A ASP* 2.6 47.4 + - - +
277A VAL 5.7 0.4 - - - +
279A TYR* 2.8 44.6 + + + -
296A ILE* 2.9 21.3 + - + +
299A LEU* 1.3 91.7 - - + +
301A LYS* 1.3 72.4 + - - +
302A GLN* 3.1 17.9 + - + +
660B ILE* 6.2 0.4 - - + -
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Residues in contact with LYS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 5.6 8.7 - - - +
98A ARG 5.9 1.4 - - - +
117A PRO* 3.9 21.0 - - + +
119A GLU* 6.2 0.2 - - - +
120A GLU* 4.2 5.9 - - - +
275A ASP* 4.9 7.0 - - - +
297A CYS 2.8 14.0 + - - +
298A HIS* 3.1 41.1 + - - +
299A LEU 4.3 6.3 - - - +
300A HIS* 1.3 80.3 - - - +
302A GLN* 1.3 71.2 + - - +
587A LYS* 5.0 6.1 - - - +
659B PRO* 6.5 0.7 - - + -
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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