Contacts of the helix formed by residues 60 - 74 (chain A) in PDB entry 1GZD
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 THR 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.9 10.4 - - + -
22A ASP 5.8 0.9 - - - +
23A LEU* 4.5 10.3 - - + -
28A LEU* 4.0 21.8 - - + -
35A ARG* 4.7 1.6 - - - +
39A PHE* 3.8 10.1 - - - -
59A VAL* 1.3 80.2 - - - +
61A GLU* 1.3 68.4 + - - +
62A ALA* 3.6 9.7 + - - +
63A VAL* 3.0 25.6 + - - +
64A MET* 2.9 24.1 + - - +
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Residues in contact with GLU 61 (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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32A ASP* 4.0 5.6 - - - +
38A HIS* 3.5 33.2 + - - +
39A PHE* 3.6 20.5 - - + -
60A THR* 1.3 70.4 - - - +
62A ALA* 1.3 69.3 + - - +
64A MET* 3.2 6.6 + - - +
65A GLN* 2.9 25.4 + - - +
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Residues in contact with ALA 62 (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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15A TRP* 4.7 11.7 - - + +
60A THR* 3.2 9.2 + - - +
61A GLU* 1.3 82.3 - - - +
63A VAL* 1.3 64.0 + - - +
65A GLN* 3.1 6.2 + - - +
66A MET* 3.0 35.6 + - + +
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.6 2.7 - - + -
15A TRP* 3.4 38.6 - - + -
23A LEU* 5.3 0.2 - - + -
59A VAL* 3.6 19.7 - - + -
60A THR* 3.0 30.8 + - - +
62A ALA* 1.3 77.4 - - - +
64A MET* 1.3 51.2 + - - +
66A MET* 3.2 10.7 + - + +
67A LEU* 2.8 47.6 + - + +
325A TRP* 3.9 26.0 - - + -
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Residues in contact with MET 64 (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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39A PHE* 3.7 21.8 - - + -
54A TYR* 4.4 13.0 - - + -
59A VAL* 3.6 25.8 - - + -
60A THR 2.9 19.2 + - - +
61A GLU* 3.7 5.4 - - - +
63A VAL* 1.3 75.4 - - - +
65A GLN* 1.3 57.8 + - - +
67A LEU* 3.3 16.1 + - + +
68A VAL* 2.9 36.2 + - + +
318A LEU* 3.6 32.3 - - + -
321A LEU* 5.1 6.5 - - + -
322A LEU* 3.9 19.1 - - + -
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Residues in contact with GLN 65 (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 GLU 2.9 17.0 + - - +
62A ALA* 3.6 6.3 - - - +
64A MET* 1.3 77.3 - - - +
66A MET* 1.3 57.9 + - + +
68A VAL* 3.1 13.8 + - - +
69A ASP* 2.9 44.5 + - - +
312A GLU* 4.8 15.5 - - - +
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Residues in contact with MET 66 (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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8A GLN* 4.6 4.3 - - + +
11A LYS* 4.2 41.1 - - + -
12A LEU* 3.7 31.5 - - + +
15A TRP* 3.9 39.3 - - + +
62A ALA* 3.0 24.9 + - + +
63A VAL* 3.6 16.2 - - + +
65A GLN* 1.3 77.0 - - + +
67A LEU* 1.3 59.8 + - - +
69A ASP* 3.4 13.4 + - - +
70A LEU* 3.1 21.7 + - - +
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Residues in contact with LEU 67 (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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12A LEU* 4.4 17.3 - - + -
59A VAL* 4.4 4.5 - - + -
63A VAL* 2.8 40.9 + - + +
64A MET* 3.5 24.9 - - + +
66A MET* 1.3 69.9 - - - +
68A VAL* 1.3 65.6 + - - +
70A LEU* 3.4 7.4 + - + +
71A ALA 3.3 10.9 + - - -
321A LEU* 3.2 65.6 - - + +
322A LEU* 5.0 1.6 - - + -
324A ILE* 5.0 7.0 - - + -
325A TRP* 4.4 25.6 - - + +
329A PHE* 5.2 0.9 - - + -
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Residues in contact with VAL 68 (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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64A MET* 2.9 22.3 + - + +
65A GLN* 3.1 15.2 + - - +
67A LEU* 1.3 74.0 - - - +
69A ASP* 1.3 69.0 + - - +
71A ALA* 3.0 13.7 + - - +
72A LYS* 3.1 18.6 + - + +
311A LEU* 4.2 24.5 - - + +
312A GLU* 4.1 39.5 - - + +
318A LEU* 5.1 6.3 - - + -
321A LEU* 4.0 17.7 - - + -
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Residues in contact with ASP 69 (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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8A GLN* 4.0 21.4 - - + +
65A GLN* 2.9 35.6 + - - +
66A MET* 3.6 16.1 - - - +
67A LEU 3.3 0.2 - - - -
68A VAL* 1.3 78.8 - - - +
70A LEU* 1.3 56.0 + - - +
72A LYS* 3.5 11.4 + - - +
73A SER* 3.0 31.4 + - - -
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Residues in contact with LEU 70 (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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3A LEU* 4.1 13.2 - - + -
6A ASN* 3.5 32.3 - - - +
8A GLN* 4.2 9.6 - - + +
9A PHE* 3.8 22.9 - - + +
12A LEU* 4.3 16.8 - - + -
66A MET 3.1 13.8 + - - +
67A LEU* 3.6 14.4 - - + +
68A VAL 3.2 0.4 - - - -
69A ASP* 1.3 77.0 - - - +
71A ALA* 1.3 56.1 + - - +
73A SER* 3.3 1.3 + - - -
74A ARG* 2.9 37.7 + - + +
321A LEU* 5.1 3.4 - - + -
324A ILE* 4.6 14.1 - - + -
329A PHE* 5.5 0.7 - - + -
503A ILE* 3.9 24.5 - - + -
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Residues in contact with ALA 71 (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 LEU 3.3 9.4 + - - +
68A VAL 3.0 10.4 + - - +
70A LEU* 1.3 78.7 - - - +
72A LYS* 1.3 60.6 + - - +
74A ARG 3.4 1.0 + - - -
75A GLY 3.4 3.5 + - - -
76A VAL* 3.1 48.1 + - + +
311A LEU* 3.9 15.0 - - + -
317A VAL* 4.7 5.8 - - + -
321A LEU* 4.3 10.8 - - + -
499A VAL* 5.5 0.2 - - + -
503A ILE* 4.1 15.5 - - + +
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Residues in contact with LYS 72 (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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68A VAL* 3.1 18.5 + - + +
69A ASP* 3.6 15.3 - - - +
71A ALA* 1.3 73.2 - - - +
73A SER* 1.3 65.4 + - - +
75A GLY* 3.1 14.2 + - - -
76A VAL 4.9 0.4 - - - +
77A GLU* 3.5 32.6 - - - +
311A LEU* 4.0 12.3 - - + +
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Residues in contact with SER 73 (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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6A ASN* 3.0 23.9 + - - -
7A PRO* 5.3 0.7 - - - +
8A GLN* 3.9 21.2 + - - +
69A ASP 3.0 16.5 + - - -
70A LEU 3.6 3.4 - - - -
72A LYS* 1.3 80.9 - - - +
74A ARG* 1.3 60.1 + - - +
75A GLY 3.3 1.5 + - - -
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Residues in contact with ARG 74 (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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2A ALA* 3.3 37.2 + - - +
3A LEU* 4.0 20.0 - - - +
6A ASN* 3.8 21.7 - - - +
70A LEU* 2.9 24.2 + - + +
71A ALA 4.2 2.9 - - - +
72A LYS 3.1 0.6 - - - -
73A SER* 1.3 77.9 - - - +
75A GLY* 1.3 59.4 + - - +
76A VAL 3.5 1.8 - - - -
502A VAL* 3.1 35.8 + - + +
503A ILE* 3.2 37.3 + - + +
505A ASP* 3.8 17.8 + - - +
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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