Contacts of the helix formed by residues 56 - 68 (chain A) in PDB entry 1GNU
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ASP 4.2 6.7 - - - +
55A LEU* 1.3 76.8 - - - +
57A VAL* 1.3 65.0 + - - +
58A GLY* 3.4 3.3 + - - -
59A GLN* 2.9 44.2 + - - +
60A PHE* 2.9 22.7 + - - +
87A THR 3.7 11.6 + - - +
88A SER* 4.9 7.9 - - - +
89A ALA 3.5 8.7 - - - +
90A THR* 4.2 5.2 - - + +
91A MET* 4.6 1.3 - - - -
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU 3.9 0.4 + - - -
56A THR* 1.3 71.3 - - - +
58A GLY* 1.3 57.2 + - - +
60A PHE* 3.2 1.9 + - - +
61A TYR* 2.9 47.3 + - + +
78A PHE* 4.4 6.1 - - + -
85A PRO* 4.1 15.3 - - + -
86A PRO 3.3 28.5 - - - +
87A THR* 3.6 5.8 + - - -
89A ALA* 2.9 28.6 + - + +
90A THR 4.7 1.3 - - - -
91A MET* 4.2 14.1 - - - -
94A LEU* 4.0 25.6 - - + -
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Residues in contact with GLY 58 (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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56A THR* 3.2 2.0 - - - -
57A VAL* 1.3 76.6 - - - +
59A GLN* 1.3 60.3 + - - +
61A TYR* 3.4 8.2 - - - +
62A PHE* 3.0 21.7 + - - +
87A THR* 2.9 36.7 + - - +
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Residues in contact with GLN 59 (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 ASP 4.4 1.2 - - - +
55A LEU* 3.6 25.2 - - + +
56A THR* 2.9 50.8 + - - +
58A GLY* 1.3 75.3 - - - +
60A PHE* 1.3 64.5 + - - +
62A PHE* 3.1 9.7 + - - +
63A LEU* 3.0 27.5 + - + +
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Residues in contact with PHE 60 (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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31A VAL* 4.4 4.5 - - + -
33A VAL* 3.9 26.7 - - + -
49A TYR* 4.1 19.3 - + + -
51A VAL* 3.9 19.1 - - + -
55A LEU* 3.9 24.0 - - + +
56A THR 2.9 14.9 + - - +
57A VAL* 3.2 4.5 + - - +
59A GLN* 1.3 77.1 - - - +
61A TYR* 1.3 56.1 + - - +
63A LEU* 3.1 12.3 + - + +
64A ILE* 2.9 60.8 + - + +
78A PHE* 3.9 16.8 - + - -
91A MET* 3.9 23.6 - - + -
107A ILE* 3.9 14.6 - - + -
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 2.9 34.6 + - + -
58A GLY* 3.4 8.7 - - - +
60A PHE* 1.3 75.8 - - - +
62A PHE* 1.3 57.2 + - - +
64A ILE* 3.9 0.5 - - - +
65A ARG* 2.8 47.1 + - - +
76A LEU* 3.5 33.9 + - + +
77A PHE* 3.7 7.2 - - - -
78A PHE* 3.0 64.7 + + + +
84A ILE* 3.8 15.6 - - - +
85A PRO 4.6 5.6 - - - -
87A THR* 4.3 19.5 - - + -
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Residues in contact with PHE 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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58A GLY 3.0 13.9 + - - +
59A GLN* 3.1 12.7 + - - +
61A TYR* 1.3 75.5 - - - +
63A LEU* 1.3 71.9 + - + +
65A ARG* 3.8 14.0 - - + +
66A LYS* 3.1 50.7 + - + +
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Residues in contact with LEU 63 (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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49A TYR* 6.4 0.9 - - + -
51A VAL* 6.4 0.2 - - + -
55A LEU* 4.3 21.8 - - + -
59A GLN* 3.0 17.0 + - + +
60A PHE* 3.1 21.7 + - + +
62A PHE* 1.3 81.6 - - + +
64A ILE* 1.3 61.7 + - + +
66A LYS* 3.3 6.6 + - + +
67A ARG* 3.0 34.9 + - + +
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Residues in contact with ILE 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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33A VAL* 4.6 5.4 - - + -
44A LEU* 4.3 22.4 - - + -
49A TYR* 3.7 37.9 - - + +
60A PHE* 2.9 44.5 + - + +
61A TYR 4.0 2.0 - - - +
63A LEU* 1.3 71.4 - - + +
65A ARG* 1.3 67.0 + - - +
67A ARG* 3.1 8.7 + - - +
68A ILE* 3.0 33.6 + - + +
76A LEU* 4.7 3.6 - - + -
78A PHE* 3.9 29.2 - - + -
109A TYR* 5.0 4.5 - - + -
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Residues in contact with ARG 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 TYR* 2.8 39.6 + - - +
62A PHE* 3.8 12.1 - - + +
64A ILE* 1.3 72.2 - - - +
66A LYS* 1.3 59.5 + - + +
68A ILE* 3.2 9.4 + - - +
69A HIS 2.8 26.0 + - - -
70A LEU* 2.9 32.0 + - + +
71A ARG 2.4 33.7 + - - -
72A ALA* 3.6 17.3 + - - +
74A ASP 2.8 24.0 + - - -
75A ALA* 4.8 0.4 - - - +
76A LEU* 3.5 35.4 + - + +
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Residues in contact with LYS 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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62A PHE* 3.1 41.9 + - + +
63A LEU* 3.7 6.5 - - + +
65A ARG* 1.3 82.3 - - + +
67A ARG* 1.3 58.8 + - - +
69A HIS* 3.6 18.5 + - - +
70A LEU 4.8 2.7 - - - -
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Residues in contact with ARG 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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43A ASP 5.4 0.5 - - - +
44A LEU* 4.0 9.2 - - + -
45A ASP* 2.2 57.9 + - - +
46A LYS* 3.9 23.1 - - - +
49A TYR* 3.3 28.2 + - - -
63A LEU* 3.0 22.3 + - + +
64A ILE* 3.1 10.7 + - - +
66A LYS* 1.3 78.8 - - - +
68A ILE* 1.3 59.4 + - - +
69A HIS* 3.3 13.1 + - - -
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Residues in contact with ILE 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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41A ILE* 4.2 3.8 - - + -
42A GLY* 4.1 18.5 + - - +
43A ASP 3.7 19.7 - - - +
44A LEU* 3.6 31.4 - - + -
45A ASP 5.3 0.2 - - - +
64A ILE* 3.0 20.7 + - + +
65A ARG* 3.7 5.8 - - - +
67A ARG* 1.3 76.2 - - - +
69A HIS* 1.3 71.0 + - - +
70A LEU* 3.8 30.5 - - + +
76A LEU* 4.3 9.6 - - + -
109A TYR* 3.7 32.1 - - + +
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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