Contacts of the helix formed by residues 310 - 323 (chain A) in PDB entry 4GSA
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 PRO 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA* 5.5 4.5 - - + +
90A GLY 4.4 10.3 - - - +
91A THR 3.4 15.5 - - - +
92A SER* 4.0 9.2 - - - -
93A PHE* 3.4 45.5 - - + +
97A CYS* 4.1 8.5 - - - -
99A LEU* 3.8 15.4 - - + +
308A GLY 4.2 1.8 - - - +
309A ASN* 1.3 82.1 - - + +
311A LEU* 1.3 63.1 + - + +
313A MET* 3.5 5.6 + - + -
314A THR* 2.9 29.7 + - - -
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Residues in contact with LEU 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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83A LEU* 3.6 18.2 - - + +
86A ALA* 4.0 11.2 - - + -
87A MET* 3.7 49.6 - - + +
90A GLY 5.0 1.1 - - - +
91A THR* 3.8 33.6 + - + +
279A LEU* 3.7 19.3 - - + -
309A ASN* 3.0 10.2 + - - +
310A PRO* 1.3 75.1 - - - +
312A ALA* 1.3 65.8 + - - +
314A THR* 3.1 6.5 + - - -
315A ALA* 2.9 19.1 + - - +
83B LEU* 5.4 0.4 - - + -
279B LEU* 4.2 16.4 - - + -
311B LEU* 5.0 7.2 - - + -
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Residues in contact with ALA 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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103A LEU* 5.1 0.7 - - - +
275A ILE 4.7 0.2 - - - +
279A LEU* 3.6 17.6 - - + +
280A PRO* 4.2 5.8 - - + +
281A VAL* 3.2 33.4 - - + +
308A GLY 6.1 0.2 - - - +
309A ASN* 3.1 26.0 + - - +
311A LEU* 1.3 77.8 - - - +
313A MET* 1.3 69.7 + - + +
315A ALA* 3.2 3.1 + - - +
316A GLY* 2.9 21.1 + - - -
280B PRO* 5.7 0.9 - - + -
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Residues in contact with MET 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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99A LEU* 3.8 26.7 - - + +
100A GLU* 4.1 18.4 - - + -
103A LEU* 3.9 25.3 - - + +
119A PHE* 4.0 32.3 - - + -
281A VAL* 4.2 17.5 - - + -
308A GLY* 3.6 28.7 - - - +
309A ASN 3.1 17.4 + - - +
310A PRO* 3.8 2.9 - - + +
311A LEU 3.3 0.6 - - - -
312A ALA* 1.3 80.8 - - + +
314A THR* 1.3 57.9 + - - +
316A GLY* 3.3 0.7 + - - -
317A ILE* 2.8 36.8 + - + +
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Residues in contact with THR 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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82A ALA* 3.7 39.7 - - + +
83A LEU* 4.2 8.3 - - + -
86A ALA* 3.8 13.5 - - + +
99A LEU* 3.4 16.6 - - - +
310A PRO 2.9 18.2 + - - -
311A LEU 3.4 8.3 - - - -
313A MET* 1.3 74.3 - - - +
315A ALA* 1.3 65.9 + - - +
317A ILE* 3.2 9.4 + - - +
318A LYS* 2.9 24.2 + - + +
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Residues in contact with ALA 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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79A VAL* 4.7 9.0 - - + +
83A LEU* 3.9 17.9 - - + +
276A GLY 3.2 22.7 - - - +
277A GLY* 4.5 5.4 - - - +
279A LEU* 4.1 13.7 - - + -
311A LEU 2.9 12.0 + - - +
312A ALA 3.5 5.8 - - - +
314A THR* 1.3 77.6 - - - +
316A GLY* 1.3 60.6 + - - +
318A LYS* 3.9 1.8 - - - +
319A THR* 2.8 31.3 + - - -
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Residues in contact with GLY 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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103A LEU* 4.3 11.4 - - - -
275A ILE* 3.2 28.8 + - - -
312A ALA 2.9 12.3 + - - -
313A MET 3.8 1.8 - - - -
315A ALA* 1.3 73.1 - - - +
317A ILE* 1.3 67.4 + - - +
319A THR* 3.3 3.8 + - - -
320A LEU* 3.0 30.1 + - - +
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Residues in contact with ILE 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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99A LEU* 3.8 40.6 - - + +
102A VAL* 3.8 21.5 - - + -
103A LEU* 3.7 21.2 - - + +
106A MET* 3.8 21.7 - - - +
313A MET 2.8 29.7 + - - +
314A THR* 3.2 6.7 + - - +
316A GLY* 1.3 77.8 - - - +
318A LYS* 1.3 65.0 + - + +
320A LEU 3.3 0.2 + - - -
321A GLU* 3.1 35.6 + - - +
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Residues in contact with LYS 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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78A GLU* 3.7 46.2 - - + +
79A VAL* 4.0 19.5 - - + -
82A ALA* 4.3 16.3 - - + +
314A THR* 2.9 16.9 + - + +
315A ALA* 4.0 3.1 - - - +
317A ILE* 1.3 78.9 - - + +
319A THR* 1.3 63.2 + - - +
321A GLU* 3.2 26.8 + - - +
322A LEU* 3.1 29.1 + - + +
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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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69A PRO 5.3 2.5 - - - +
71A ILE* 4.7 2.0 - - + -
72A CYS* 3.8 23.8 - - - -
79A VAL* 4.1 13.3 - - - +
274A ILE* 3.8 34.1 - - + +
277A GLY* 3.4 19.6 + - - -
315A ALA 2.8 21.8 + - - -
316A GLY 3.8 3.8 - - - -
318A LYS* 1.3 76.1 - - - +
320A LEU* 1.3 63.9 + - + +
322A LEU* 3.2 12.4 + - - +
323A LEU* 3.2 16.7 + - + +
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Residues in contact with LEU 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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103A LEU* 4.0 22.2 - - + -
106A MET* 3.5 33.9 - - + +
107A VAL* 4.5 5.8 - - + -
251A PHE* 3.8 51.4 - - + -
255A TYR* 3.8 14.4 + - + +
274A ILE* 5.0 2.0 - - + +
275A ILE* 4.8 14.8 - - + -
316A GLY 3.0 18.3 + - - +
319A THR* 1.3 80.7 - - - +
321A GLU* 1.3 57.6 + - - +
323A LEU* 3.5 10.5 + - + +
324A ARG* 3.1 28.2 + - - +
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Residues in contact with GLU 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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106A MET* 3.8 15.5 - - + +
317A ILE* 3.1 30.3 + - - +
318A LYS* 3.5 35.1 + - + +
319A THR 3.2 0.2 - - - -
320A LEU* 1.3 74.8 - - - +
322A LEU* 1.3 66.2 + - + +
324A ARG* 3.6 17.7 + - - +
325A GLN* 3.0 28.2 + - - +
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Residues in contact with LEU 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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72A CYS* 3.9 17.3 - - + -
76A HIS* 3.5 42.2 - - + +
78A GLU* 4.0 29.8 - - + +
79A VAL* 4.0 14.4 - - + -
318A LYS* 3.1 17.1 + - + +
319A THR 3.2 6.5 + - - +
321A GLU* 1.3 79.4 - - + +
323A LEU* 1.3 60.8 + - - +
325A GLN* 3.2 28.5 + - + +
328A THR* 3.7 4.0 + - - -
412A LEU* 5.0 8.2 - - + +
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Residues in contact with LEU 323 (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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71A ILE* 4.1 26.0 - - + -
72A CYS* 4.3 10.3 - - - -
251A PHE* 4.0 18.4 - - + +
255A TYR* 4.2 7.1 - - + -
274A ILE* 4.0 23.3 - - + -
319A THR* 3.2 18.0 + - + +
320A LEU* 3.8 11.4 - - + +
321A GLU 3.4 0.2 - - - -
322A LEU* 1.3 70.7 - - - +
324A ARG* 1.3 59.6 + - - +
325A GLN 3.0 7.1 - - - +
328A THR* 3.0 42.1 + - + +
329A TYR* 3.7 30.0 - - - +
412A LEU* 4.4 7.4 - - + -
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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