Contacts of the helix formed by residues 310 - 322 (chain A) in PDB entry 5W0P
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 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.6 18.4 - - - +
135A ARG* 3.3 26.0 + - - +
253A MET* 5.1 1.9 - - - +
257A TYR* 4.0 8.5 + - - -
306A TYR 2.6 27.2 + - - +
307A ILE 3.0 11.0 + - - +
309A MET* 1.3 77.7 - - - +
311A LYS* 1.3 59.2 + - - +
312A GLN 3.5 0.2 - - - -
313A PHE* 4.0 6.4 - - + -
314A ARG* 3.0 30.5 + - - +
2076A MET* 3.4 33.9 - - + +
2078A LEU* 6.0 0.7 - - - +
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Residues in contact with LYS 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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245A LYS* 5.4 10.1 - - - +
249A GLU* 5.6 13.4 - - - +
309A MET 4.4 5.4 - - - +
310A ASN* 1.3 71.4 - - - +
312A GLN* 1.3 67.3 + - - +
314A ARG* 3.8 33.5 - - - +
315A ASN* 3.0 35.7 + - - +
2075A VAL 5.3 7.0 - - - +
2076A MET* 3.7 14.8 + - - +
33B GLU* 6.0 0.4 + - - -
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Residues in contact with GLN 312 (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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67A LYS* 3.2 31.5 + - - +
68A LEU* 3.6 20.9 - - + +
70A THR* 5.3 0.2 + - - -
73A ASN* 4.1 3.8 + - - +
310A ASN 3.5 0.2 - - - -
311A LYS* 1.3 78.8 - - - +
313A PHE* 1.3 63.9 + - - +
315A ASN* 3.9 4.5 - - - +
316A CYS* 3.3 32.2 + - - -
2072A ASP* 3.5 32.9 - - + +
2073A ILE* 3.4 25.3 - - - +
2076A MET* 3.3 29.4 - - + +
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Residues in contact with PHE 313 (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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58A THR* 4.7 9.2 - - + -
62A THR* 4.5 11.2 - - + -
68A LEU* 4.2 28.5 - - + -
73A ASN* 3.4 32.8 - - + -
76A LEU* 3.6 32.1 - - + -
77A LEU* 5.1 4.3 - - + -
307A ILE* 3.4 39.3 - - + +
310A ASN* 3.6 11.1 + - + +
311A LYS 3.3 0.2 - - - -
312A GLN* 1.3 76.9 - - - +
314A ARG* 1.3 65.5 + - - +
316A CYS* 3.4 2.6 + - - +
317A MET* 3.0 40.4 + - + +
2076A MET* 3.3 28.5 - - - -
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Residues in contact with ARG 314 (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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307A ILE 4.5 0.6 + - - -
308A MET* 3.4 28.5 - - + +
309A MET* 5.1 6.6 + - - +
310A ASN 3.0 18.7 + - - +
311A LYS* 3.8 38.2 - - - +
312A GLN 3.4 0.2 - - - -
313A PHE* 1.3 78.6 - - - +
315A ASN* 1.3 76.0 + - - +
317A MET* 3.6 6.5 + - - +
318A LEU* 3.2 21.8 + - - +
33B GLU* 3.9 13.1 + - - -
35B TRP* 3.3 63.1 - - + +
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Residues in contact with ASN 315 (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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311A LYS* 3.0 24.9 + - - +
312A GLN* 3.9 6.1 - - - +
313A PHE 3.3 0.2 - - - -
314A ARG* 1.3 94.9 + - - +
316A CYS* 1.3 65.8 + - - +
318A LEU* 3.3 10.6 + - - +
319A THR* 3.2 25.4 + - - +
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Residues in contact with CYS 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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61A VAL* 3.9 19.9 - - + +
65A HIS* 4.2 19.6 + - + -
67A LYS* 5.0 11.0 - - - -
68A LEU* 3.7 26.5 - - + -
312A GLN* 3.3 22.5 + - - +
313A PHE 3.4 3.3 + - - +
315A ASN* 1.3 79.0 - - - +
317A MET* 1.3 60.4 + - - +
319A THR* 2.5 24.3 + - - +
320A THR* 3.1 16.2 + - - -
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Residues in contact with MET 317 (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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54A ILE* 4.7 3.6 - - + +
57A LEU* 4.2 12.6 - - + +
58A THR* 3.6 44.4 - - + +
61A VAL* 4.5 14.8 - - + -
307A ILE* 4.1 16.8 - - + -
308A MET* 3.5 32.3 - - + +
313A PHE* 3.0 29.6 + - + +
314A ARG* 3.9 5.2 - - - +
315A ASN 3.3 0.2 - - - -
316A CYS* 1.3 74.4 - - - +
318A LEU* 1.3 63.6 + - - +
320A THR* 3.4 16.5 + - - -
321A ILE* 3.4 20.0 + - - +
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Residues in contact with LEU 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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314A ARG 3.2 14.3 + - - +
315A ASN* 3.5 12.6 - - - +
316A CYS 3.2 0.2 - - - -
317A MET* 1.3 77.0 - - - +
319A THR* 1.3 57.3 + - + +
320A THR 3.1 0.4 + - - -
321A ILE* 3.2 9.2 + - + -
322A CYS* 2.8 48.7 + - - -
29B TYR* 6.3 1.1 - - + -
34B PRO* 3.7 38.4 - - + +
35B TRP* 4.4 6.7 - - + +
38B SER* 3.7 30.1 - - - +
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Residues in contact with THR 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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65A HIS* 3.8 19.6 + - + -
315A ASN 3.2 8.7 + - - +
316A CYS* 2.5 32.1 + - - -
318A LEU* 1.3 78.3 - - + +
320A THR* 1.3 55.8 + - - +
322A CYS* 3.7 6.5 - - + -
323A CYS 2.8 20.3 + - - -
324A GLY 2.9 37.6 + - - +
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Residues in contact with THR 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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57A LEU* 4.6 11.4 - - + -
60A TYR* 4.4 21.1 - - + -
61A VAL* 3.2 28.9 - - + +
65A HIS* 4.8 4.7 + - - -
316A CYS 3.1 14.7 + - - -
317A MET* 3.5 9.4 - - - -
318A LEU 3.1 0.4 - - - -
319A THR* 1.3 76.7 - - - +
321A ILE* 1.3 66.0 + - + +
322A CYS 3.2 0.2 - - - -
323A CYS* 3.1 21.0 + - - +
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Residues in contact with ILE 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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57A LEU* 6.2 6.1 - - + -
317A MET 3.6 13.5 - - - +
318A LEU* 3.2 11.9 + - + +
320A THR* 1.3 77.6 - - + +
322A CYS* 1.3 61.1 + - - +
323A CYS* 3.5 9.3 + - - -
38B SER* 4.6 21.8 - - - +
99B LEU* 4.4 22.4 - - + +
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Residues in contact with CYS 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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318A LEU* 2.8 45.1 + - - +
319A THR* 3.8 10.8 - - + +
321A ILE* 1.3 77.6 - - - +
323A CYS* 1.3 69.0 + - - +
324A GLY* 3.5 7.2 + - - +
29B TYR* 5.7 6.1 - - - -
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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