Contacts of the helix formed by residues 78 - 88 (chain G) in PDB entry 4QLC
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 ILE 78 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74G LYS* 4.3 17.5 - - + +
76G ARG* 3.7 15.9 - - + +
77G ILE* 1.3 81.7 - - - +
79G PRO* 1.4 76.5 - - + +
80G ARG* 3.8 22.4 - - + +
81G HIS* 2.8 42.0 + - + +
82G LEU 3.4 6.8 + - - -
52H SER* 4.2 12.6 - - - -
55H ALA* 4.1 4.7 - - - -
142I G 5.9 3.1 - - - +
143I A 5.8 3.1 - - - +
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Residues in contact with PRO 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G ILE* 1.4 87.5 - - + +
80G ARG* 1.3 63.0 + - - +
82G LEU* 3.1 10.9 + - + +
83G GLN* 3.0 21.7 + - - +
101G ILE* 4.2 2.8 - - + +
102G ALA 3.6 21.1 - - - +
103G GLN* 3.9 16.2 - - + +
104G GLY* 4.2 2.3 - - - -
52H SER* 4.8 4.3 - - - +
54H LYS* 3.8 25.8 - - + -
55H ALA* 3.9 12.1 - - + +
58H ILE* 3.7 23.6 - - + -
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Residues in contact with ARG 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLN 3.1 21.2 + - - -
56A LYS* 3.5 23.5 + - - +
58A THR* 3.5 19.0 - - + +
78G ILE* 3.0 20.7 + - + +
79G PRO* 1.3 78.1 - - - +
81G HIS* 1.3 61.6 + - + +
83G GLN* 3.3 3.5 + - - +
84G LEU* 3.0 58.7 + - + +
103G GLN 4.0 4.0 + - - +
104G GLY 3.2 26.1 + - - -
105G GLY* 3.8 2.2 - - - -
106G VAL 2.9 31.5 + - - +
108G PRO* 3.9 9.7 - - - +
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Residues in contact with HIS 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G ALA* 4.0 17.7 - - - +
68G ALA* 3.9 16.3 + - + +
69G ALA* 3.8 26.0 - - + +
72G ASN* 4.3 13.1 + - - +
74G LYS* 4.0 22.6 + - + +
76G ARG 3.5 16.2 - - - -
77G ILE* 3.6 10.3 - - + -
78G ILE* 2.8 47.7 + - + +
80G ARG* 1.3 80.5 - - + +
82G LEU* 1.3 59.7 + - - +
84G LEU* 3.2 7.2 + - + +
85G ALA* 2.9 33.6 + - - +
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G VAL* 3.8 15.9 - - + -
62G LEU* 5.0 2.5 - - + -
65G ALA* 3.9 17.5 - - + -
77G ILE* 4.1 14.1 - - + -
78G ILE 3.4 1.7 + - - +
79G PRO* 3.1 8.2 + - + +
81G HIS* 1.3 77.9 - - - +
83G GLN* 1.3 63.3 + - - +
85G ALA* 3.6 1.9 + - - +
86G ILE* 3.1 37.8 + - + +
101G ILE* 5.1 2.9 - - + -
51H ILE* 5.6 0.2 - - + -
55H ALA* 3.6 39.3 - - + +
58H ILE* 3.8 28.9 - - + -
59H MET* 3.8 26.0 - - + -
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Residues in contact with GLN 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G PRO 3.0 10.9 + - - +
80G ARG* 3.3 14.1 - - - +
81G HIS 3.1 0.2 - - - -
82G LEU* 1.3 74.2 - - - +
84G LEU* 1.3 67.3 + - + +
86G ILE* 3.2 4.8 + - - +
87G ARG* 3.0 57.8 + - + +
101G ILE* 3.4 30.5 + - + +
104G GLY* 3.3 29.8 - - - +
105G GLY 3.1 23.4 + - - +
106G VAL* 4.3 7.8 - - - +
107G LEU* 4.9 2.5 - - + +
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Residues in contact with LEU 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G ALA* 4.4 11.0 - - + -
72G ASN* 4.4 19.5 - - - +
80G ARG* 3.0 64.9 + - + +
81G HIS* 3.7 10.5 - - + +
83G GLN* 1.3 75.8 - - + +
85G ALA* 1.3 63.7 + - - +
88G ASN* 3.0 40.6 + - - +
107G LEU* 3.6 26.5 - - + -
108G PRO* 4.5 3.6 - - + -
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G VAL* 4.3 3.8 - - + +
64G LEU* 3.6 21.6 - - + +
65G ALA* 3.5 32.3 - - + +
68G ALA* 4.6 2.6 - - + +
81G HIS 2.9 17.0 + - - +
82G LEU* 3.7 4.7 - - - +
84G LEU* 1.3 77.0 - - - +
86G ILE* 1.3 63.7 + - + +
88G ASN* 4.0 2.1 - - - +
89G ASP* 3.3 24.3 + - - +
92G LEU* 4.8 2.0 - - + -
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Residues in contact with ILE 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR* 6.4 0.9 - - + -
61G VAL* 4.7 16.4 - - + -
82G LEU* 3.1 26.3 + - + +
83G GLN* 3.8 2.5 - - - +
85G ALA* 1.3 77.5 - - - +
87G ARG* 1.3 80.2 + - - +
89G ASP* 3.0 26.5 + - - +
92G LEU* 3.8 32.1 - - + +
93G ASN 3.3 4.3 + - - +
96G LEU* 3.6 35.7 - - + -
101G ILE* 4.0 23.1 - - + -
58H ILE* 6.3 1.6 - - + -
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Residues in contact with ARG 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLN* 3.0 45.7 + - + +
84G LEU 4.5 0.7 - - - +
86G ILE* 1.3 85.6 - - - +
88G ASN* 1.3 59.0 + - - +
89G ASP 3.3 1.0 + - - -
93G ASN* 3.1 40.9 + - - +
96G LEU* 2.7 29.1 + - - +
97G SER* 4.2 3.8 - - - +
99G VAL* 3.0 29.7 + - - +
100G THR* 4.9 0.2 - - - +
101G ILE* 3.5 19.4 - - - +
107G LEU* 3.7 32.4 - - + +
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Residues in contact with ASN 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G LEU* 3.0 32.2 + - - +
85G ALA* 4.0 2.0 - - - +
87G ARG* 1.3 76.9 - - - +
89G ASP* 1.3 59.7 + - - +
90G GLU 3.9 2.0 + - - -
107G LEU* 3.1 36.9 - - - +
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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