Contacts of the helix formed by residues 87 - 104 (chain G) in PDB entry 2GTL
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 ASP 87 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F GLU* 3.2 31.3 - - - +
59F PRO* 4.8 1.2 - - - +
62F ILE* 5.1 2.8 - - - +
84G LEU* 3.2 10.2 + - - +
85G LEU 3.3 0.2 - - - -
86G ASP* 1.3 80.7 - - - +
88G PRO* 1.3 74.2 - - - +
89G PRO* 3.0 19.5 - - - +
90G ALA* 2.9 29.9 + - + +
91G LEU 2.9 9.7 + - - -
124M ASN* 5.1 10.3 + - - +
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Residues in contact with PRO 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 4.4 0.2 - - - -
85G LEU 4.4 6.0 - - - +
86G ASP* 4.1 0.9 - - - -
87G ASP* 1.3 86.7 - - - +
89G PRO* 1.3 63.9 - - + +
91G LEU* 3.7 10.7 - - + +
92G ASP* 2.6 38.5 + - - +
122M ASP* 4.1 40.2 - - + +
123M LEU 5.6 0.2 - - - +
124M ASN* 5.3 6.3 - - - +
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Residues in contact with PRO 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F PRO* 3.5 24.6 - - + +
87G ASP* 3.0 21.5 - - - +
88G PRO* 1.3 102.0 - - + +
90G ALA* 1.3 54.4 + - - +
92G ASP* 3.3 6.8 - - + +
93G ALA* 3.0 27.7 + - - +
124M ASN* 5.0 9.4 - - - +
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Residues in contact with ALA 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F PRO* 3.4 18.5 - - + +
62F ILE* 3.8 26.5 - - + -
63F ALA* 3.9 1.6 - - - +
84G LEU* 3.9 11.4 - - + -
87G ASP* 2.9 31.7 + - + +
89G PRO* 1.3 72.8 - - - +
91G LEU* 1.3 57.4 + - - +
93G ALA* 3.0 4.7 + - - +
94G ALA* 2.7 35.3 + - - +
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Residues in contact with LEU 91 (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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81G ALA* 3.3 33.4 - - + +
84G LEU* 3.2 26.8 - - + +
85G LEU* 3.6 35.7 - - + +
87G ASP 2.9 7.2 + - - +
88G PRO* 3.7 11.7 - - + +
90G ALA* 1.3 75.4 - - - +
92G ASP* 1.3 64.6 + - - +
94G ALA* 3.1 3.8 + - + +
95G LEU* 2.8 52.3 + - + +
143G ILE* 5.3 2.7 - - + -
146G LYS* 5.9 4.5 - - - +
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Residues in contact with ASP 92 (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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88G PRO 2.6 22.5 + - - +
89G PRO* 3.3 9.4 - - + +
91G LEU* 1.3 76.3 - - - +
93G ALA* 1.3 66.7 + - - +
95G LEU* 2.9 7.2 + - - +
96G ASP* 2.8 27.2 + - - +
146G LYS* 4.0 29.4 + - - +
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Residues in contact with ALA 93 (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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58F HIS* 6.1 0.2 - - + -
59F PRO* 5.0 0.9 - - + -
60F ALA* 3.9 31.4 - - + +
63F ALA* 4.3 4.3 - - + -
67F ARG* 5.2 0.7 - - - -
89G PRO 3.0 11.0 + - - +
90G ALA 3.4 7.0 - - - +
92G ASP* 1.3 80.3 + - - +
94G ALA* 1.3 64.6 + - - +
96G ASP* 3.2 8.4 + - - +
97G HIS* 3.0 24.7 + - - +
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Residues in contact with ALA 94 (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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63F ALA* 3.7 14.1 - - + +
67F ARG* 4.4 7.7 + - - +
80G LEU* 4.2 20.4 - - + +
81G ALA* 6.0 0.7 - - - -
84G LEU* 3.7 22.4 - - + -
90G ALA 2.7 16.7 + - - +
91G LEU* 3.3 12.8 - - + +
93G ALA* 1.3 73.2 - - - +
95G LEU* 1.3 61.8 + - + +
97G HIS* 3.5 6.2 + - - +
98G LEU* 3.4 22.3 + - - +
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Residues in contact with LEU 95 (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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81G ALA* 4.2 9.6 - - + -
91G LEU* 2.8 48.6 + - + +
92G ASP 3.5 2.5 - - - +
94G ALA* 1.3 72.6 - - + +
96G ASP* 1.3 59.4 + - - +
97G HIS 3.0 1.8 - - - -
98G LEU* 2.7 33.2 + - + +
99G ALA* 2.8 11.3 + - - +
143G ILE* 3.6 27.6 - - + -
146G LYS* 4.2 41.7 - - + +
147G ILE* 3.4 30.9 - - + -
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Residues in contact with ASP 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G ASP* 2.8 20.3 + - - +
93G ALA* 3.5 12.1 - - - +
95G LEU* 1.3 71.7 - - - +
97G HIS* 1.3 57.6 + - - +
99G ALA* 2.8 31.2 + - - +
100G HIS* 3.1 32.4 + - - -
146G LYS* 5.0 5.7 - - + +
149G SER* 5.6 1.6 + - - -
150G ARG* 4.2 16.2 + - - -
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Residues in contact with HIS 97 (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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50F ARG* 3.5 36.5 + - - +
67F ARG* 3.5 41.0 + - - +
160F HEM 3.2 37.2 + - - -
93G ALA 3.0 11.9 + - - +
94G ALA 3.5 11.6 + - - +
96G ASP* 1.3 76.4 + - - +
98G LEU* 1.3 62.5 + - - +
99G ALA 3.2 0.3 + - - -
100G HIS* 3.2 14.7 + + + +
101G GLN* 3.1 47.4 + - + +
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Residues in contact with LEU 98 (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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67F ARG* 5.9 3.8 - - - -
77G GLY* 4.8 13.0 - - - +
80G LEU* 5.5 8.5 - - + -
81G ALA* 5.5 1.1 - - + -
94G ALA 3.6 11.4 - - - +
95G LEU* 2.7 30.2 + - + +
97G HIS* 1.3 78.4 - - - +
99G ALA* 1.3 59.5 + - - +
101G GLN* 3.3 22.6 + - - +
102G HIS* 2.8 33.2 + - + +
147G ILE* 3.8 33.0 - - + -
160G HEM 4.1 37.9 - - + -
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Residues in contact with ALA 99 (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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95G LEU 2.8 4.8 + - - -
96G ASP* 2.8 20.5 + - - +
98G LEU* 1.3 76.5 - - - +
100G HIS* 1.3 48.0 + - - +
102G HIS* 2.8 7.8 + - - +
103G GLU* 2.7 33.3 + - - +
146G LYS 3.8 14.1 - - - +
147G ILE 3.0 23.2 + - - +
149G SER* 4.4 3.1 - - - +
150G ARG* 3.7 28.2 - - + +
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Residues in contact with HIS 100 (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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96G ASP* 3.1 39.3 + - - -
97G HIS* 3.6 13.0 - + + +
99G ALA* 1.3 79.6 - - - +
101G GLN* 1.3 61.4 + - + +
102G HIS 3.1 1.0 + - - -
103G GLU* 3.2 28.6 + - - +
104G VAL* 3.5 19.4 + - - +
150G ARG* 3.1 39.0 + - - +
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Residues in contact with GLN 101 (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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67F ARG* 5.9 0.2 - - - -
95F GLN* 4.6 1.2 + - - -
160F HEM 3.1 32.3 + - - +
97G HIS* 3.1 33.2 + - + +
98G LEU* 3.4 29.9 - - - +
99G ALA 3.2 0.6 - - - -
100G HIS* 1.3 75.7 - - + +
102G HIS* 1.3 64.0 + - + +
104G VAL* 4.2 6.4 - - - +
105G ARG* 3.2 21.7 - - - +
160G HEM 3.7 41.4 + - + +
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Residues in contact with HIS 102 (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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98G LEU* 2.8 23.4 + - + +
99G ALA 2.8 7.9 + - - +
101G GLN* 1.3 82.4 - - + +
103G GLU* 1.3 64.7 + - - +
104G VAL 3.3 2.0 - - - -
105G ARG* 3.2 25.0 + - - +
108G VAL* 4.5 5.1 - - + +
113G PHE* 3.7 17.7 - + + -
147G ILE* 4.3 12.9 - - + +
148G SER* 5.9 0.2 - - - -
150G ARG 5.5 0.2 - - - +
151G LEU* 3.9 19.1 - - + +
160G HEM 2.0 97.3 + + + -
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Residues in contact with GLU 103 (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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99G ALA 2.7 15.1 + - - +
100G HIS* 3.2 24.5 + - - +
102G HIS* 1.3 78.6 - - - +
104G VAL* 1.3 66.2 + - + +
105G ARG 3.1 8.7 + - - +
106G GLU* 4.4 2.3 + - - -
150G ARG* 3.3 54.7 + - + +
151G LEU* 4.6 5.2 - - - +
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Residues in contact with VAL 104 (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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100G HIS 3.7 16.2 - - - +
101G GLN* 4.2 11.7 - - - +
103G GLU* 1.3 84.1 - - + +
105G ARG* 1.3 68.3 + - - +
106G GLU 3.6 4.7 + - - -
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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