Contacts of the helix formed by residues 68 - 80 (chain B) in PDB entry 6GHM
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 GLN 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B ILE* 3.2 19.3 + - + +
66B HIS* 3.2 8.2 - - - +
67B GLY* 1.3 74.3 - - - +
69B TYR* 1.3 64.3 + - - +
70B TYR 3.2 2.9 - - - -
71B ASP* 2.9 41.3 + - + +
72B LEU* 3.0 10.7 + - - +
97B GLY* 4.9 5.8 - - - -
103B THR* 4.2 0.9 - - - -
269B ALA* 3.6 24.7 - - + +
270B PRO 3.0 20.2 + - - -
271B ASN 4.4 1.8 + - - -
272B TYR* 3.7 8.5 - - - -
273B CYS* 3.7 22.2 + - - -
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Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 2.7 34.7 + - + +
17B LEU 3.9 0.3 + - - -
19B VAL* 3.3 33.0 - - + -
67B GLY 3.1 4.9 + - - -
68B GLN* 1.3 74.4 - - - +
70B TYR* 1.3 65.1 + + - +
72B LEU* 3.1 9.2 + - + +
73B LEU* 3.0 46.0 + - + +
99B GLN* 3.7 24.8 - - + +
102B GLU* 3.5 31.9 - - + -
103B THR* 3.5 31.9 - - - +
106B LEU* 3.6 27.8 - - + +
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.5 28.3 - - + +
20B GLN* 3.7 9.3 + - - -
21B GLY* 2.8 45.4 + - - -
22B SER 5.5 1.6 - - - -
68B GLN 3.2 1.4 - - - -
69B TYR* 1.3 80.1 - + - +
71B ASP* 1.3 60.1 + - - +
73B LEU* 3.6 18.8 + - + +
74B ARG* 3.2 28.6 + - - +
99B GLN* 3.2 36.2 + - - -
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Residues in contact with ASP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 6.1 0.7 - - + -
68B GLN* 2.9 39.2 + - + +
70B TYR* 1.3 78.2 - - - +
72B LEU* 1.3 61.0 + - - +
74B ARG* 2.9 37.8 + - - +
75B LEU* 2.9 27.1 + - - +
268B SER 4.6 4.0 - - - +
270B PRO* 3.3 27.4 - - + +
296B LEU* 3.5 8.7 - - + +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 4.2 15.5 - - + +
68B GLN 3.0 10.9 + - - +
69B TYR* 3.1 20.6 + - + +
71B ASP* 1.3 76.8 - - - +
73B LEU* 1.3 61.4 + - - +
75B LEU* 3.1 16.5 + - + +
76B PHE* 3.1 45.2 + - + -
89B PHE* 3.6 30.3 - - + -
103B THR* 4.1 24.5 - - + +
106B LEU* 4.3 8.1 - - + -
107B LEU* 3.9 20.9 - - + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 3.9 29.2 - - + +
19B VAL* 4.6 9.0 - - + +
69B TYR* 3.0 55.6 + - + +
70B TYR* 3.8 23.3 - - + +
72B LEU* 1.3 75.5 - - - +
74B ARG* 1.3 57.3 + - - +
76B PHE* 3.2 7.5 + - + +
77B GLU* 2.8 32.8 + - + +
81B PHE* 4.0 12.2 - - + -
106B LEU* 3.9 10.8 - - + -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR 3.2 14.4 + - - +
71B ASP* 2.9 34.9 + - - +
73B LEU* 1.3 76.4 - - + +
75B LEU* 1.3 63.1 + - - +
77B GLU* 3.1 8.1 + - - +
78B TYR* 2.9 25.1 + - - +
270B PRO* 3.3 17.0 - - - +
296B LEU* 3.9 20.0 - - + +
297B LYS* 2.6 40.8 + - - +
298B PRO 3.7 11.5 + - - -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B CYS* 4.2 14.6 - - + -
65B ILE* 3.8 29.4 - - + -
71B ASP 2.9 17.5 + - - +
72B LEU* 3.3 18.2 - - + +
74B ARG* 1.3 76.7 - - - +
76B PHE* 1.3 60.4 + - + +
78B TYR* 3.8 1.3 - - - +
79B GLY* 2.7 28.8 + - - -
87B TYR* 4.0 1.5 + - - -
268B SER* 3.8 20.4 - - - +
281B ALA 4.9 0.9 - - - -
282B MET* 3.5 41.9 - - + +
296B LEU* 3.6 27.6 - - + +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU* 3.1 41.1 + - + -
73B LEU* 3.2 3.1 + - - +
75B LEU* 1.3 79.3 - - + +
77B GLU* 1.3 56.1 + - - +
80B GLY* 2.6 36.0 + - - -
81B PHE* 3.4 42.4 + + + -
82B PRO* 3.7 20.2 - - + -
87B TYR* 3.6 31.0 - + - -
89B PHE* 3.7 29.2 - + - -
106B LEU* 4.1 7.2 - - + -
107B LEU* 4.3 1.3 - - + -
110B TYR* 3.9 17.9 - + - -
118B PHE* 3.9 17.7 - + - -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 2.8 20.0 + - + +
74B ARG* 3.1 8.7 + - - +
76B PHE* 1.3 75.0 - - - +
78B TYR* 1.3 62.2 + - - +
80B GLY* 3.9 3.8 + - - -
81B PHE* 3.6 25.1 - - + -
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 5.3 0.2 + - - -
74B ARG 2.9 15.9 + - - +
75B LEU* 3.8 2.7 - - - +
77B GLU* 1.3 79.4 - - - +
79B GLY* 1.3 61.3 + - - +
80B GLY 3.6 0.2 + - - -
282B MET* 4.9 2.0 - - - -
294B GLN* 3.3 46.6 + - + +
295B ILE 3.2 30.3 + - - -
296B LEU* 4.0 14.1 - - + -
957C ASP* 4.7 8.0 + - - -
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 3.7 9.9 + - - -
75B LEU 2.7 16.2 + - - -
78B TYR* 1.3 75.2 - - - +
80B GLY* 1.3 52.9 + - - +
85B SER* 2.7 28.6 + - - -
87B TYR* 3.2 16.9 + - - -
282B MET* 4.4 4.9 - - - -
294B GLN* 4.0 15.7 - - - -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PHE* 2.6 16.6 + - - +
77B GLU 3.9 3.6 + - - -
78B TYR 3.4 3.0 + - - -
79B GLY* 1.3 74.1 - - - +
81B PHE* 1.3 66.9 + - - -
82B PRO* 4.0 0.3 - - - +
84B GLU* 4.1 21.3 - - - -
85B SER 4.5 0.3 + - - -
87B TYR* 2.5 30.1 + - - -
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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