Contacts of the helix formed by residues 102 - 114 (chain G) in PDB entry 5A15
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 GLU 102 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G LEU* 3.5 11.1 - - + +
100G PHE* 3.1 27.8 - - + -
101G PRO* 1.3 97.3 - - + +
103G LYS* 1.3 62.9 + - - +
104G GLY 3.4 2.7 - - - +
105G ARG* 3.0 39.1 + - - -
106G LEU* 3.2 15.4 + - - +
83H ARG* 3.0 33.3 + - - -
84H TYR* 4.3 0.7 + - - -
97H PRO* 3.8 19.3 - - + +
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Residues in contact with LYS 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G LEU* 3.5 31.9 - - + -
100G PHE* 3.9 21.3 - - + +
101G PRO 3.8 2.8 + - - -
102G GLU* 1.3 72.7 - - - +
104G GLY* 1.3 60.9 + - - +
106G LEU* 3.2 5.3 + - - +
107G LYS* 3.0 28.1 + - - +
121G LEU 5.9 0.6 + - - -
122G LEU* 4.4 31.6 + - + +
124G PRO* 6.1 3.2 - - - +
98H ASP* 4.3 7.2 + - - +
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Residues in contact with GLY 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G GLU* 3.4 1.2 - - - +
103G LYS* 1.3 77.8 - - - +
105G ARG* 1.3 60.7 + - - +
107G LYS* 3.4 11.4 - - - +
108G ARG* 3.2 18.9 + - - +
95H VAL* 3.8 17.6 - - - +
96H LEU 5.9 0.4 - - - -
98H ASP* 5.0 7.4 + - - -
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Residues in contact with ARG 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ASP* 3.7 8.7 + - - +
81G LEU* 3.7 20.3 - - + +
102G GLU* 3.0 25.4 + - + +
103G LYS 3.2 0.6 - - - -
104G GLY* 1.3 75.8 - - - +
106G LEU* 1.3 64.5 + - - +
108G ARG* 3.0 16.9 + - - +
109G GLU* 3.0 19.1 + - - +
83H ARG* 3.0 40.6 - - - +
84H TYR* 3.9 17.1 - - - -
87H ASP* 2.4 34.4 + - - +
95H VAL* 2.9 36.2 + - + +
96H LEU 3.9 7.6 - - - +
97H PRO* 3.9 19.1 - - + -
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Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G LEU* 3.5 38.7 - - + +
84G TYR* 3.8 26.5 - - + +
85G ILE* 3.9 18.1 - - + +
94G VAL* 5.4 3.6 - - + -
96G LEU* 4.3 20.2 - - + -
100G PHE* 4.4 10.8 - - + -
102G GLU 3.2 15.1 + - - +
103G LYS 3.2 5.8 + - - +
105G ARG* 1.3 78.6 - - - +
107G LYS* 1.3 57.6 + - - +
109G GLU* 3.3 7.3 + - + +
110G ALA* 3.0 26.3 + - - +
118G LEU* 5.6 2.7 - - + -
122G LEU* 4.0 20.6 - - + -
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Residues in contact with LYS 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G LYS 3.0 13.0 + - - +
104G GLY* 3.4 14.4 - - - +
105G ARG 3.1 0.2 - - - -
106G LEU* 1.3 78.1 - - - +
108G ARG* 1.3 56.4 + - - +
110G ALA* 3.1 5.2 + - - +
111G GLU* 3.0 47.1 + - - +
119G VAL* 4.0 20.0 - - + +
122G LEU* 3.7 26.1 - - + +
123G THR* 3.5 33.5 + - - +
124G PRO* 5.9 1.2 - - - +
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Residues in contact with ARG 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ARG* 4.2 8.0 - - - +
104G GLY 3.2 9.4 + - - +
105G ARG* 3.0 12.4 + - - +
107G LYS* 1.3 76.1 - - - +
109G GLU* 1.3 67.6 + - - +
111G GLU* 3.2 39.0 + - - +
112G TYR* 3.1 28.2 + - - +
91H ASP* 3.6 41.4 + - - +
93H GLN* 4.2 30.7 + - + +
95H VAL* 4.1 23.3 - - + +
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Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G ARG* 2.8 53.1 + - - +
78G ASP* 4.2 17.6 + - - +
81G LEU* 3.9 27.3 - - + +
82G PHE 5.8 0.2 - - - +
85G ILE* 4.1 16.2 - - + -
105G ARG* 3.0 19.3 + - - +
106G LEU* 3.3 8.0 + - - +
108G ARG* 1.3 77.5 - - - +
110G ALA* 1.3 58.0 + - - +
112G TYR* 3.1 2.3 + - - +
113G PHE* 2.8 42.6 + - + -
87H ASP* 4.6 7.6 - - - +
91H ASP* 5.0 0.7 - - - +
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Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ILE* 3.9 7.8 - - - +
106G LEU 3.0 13.0 + - - +
107G LYS* 3.1 13.0 + - - +
109G GLU* 1.3 77.4 - - - +
111G GLU* 1.3 51.3 + - - +
113G PHE* 3.4 3.5 + - - +
114G GLN 2.8 28.1 + - - -
115G LEU* 3.1 13.7 + - - +
118G LEU* 3.7 34.1 - - + -
119G VAL* 3.9 15.7 - - + +
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Residues in contact with GLU 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G LYS* 3.0 40.2 + - - +
108G ARG* 3.2 37.9 + - - +
109G GLU 3.2 0.2 - - - -
110G ALA* 1.3 73.4 - - - +
112G TYR* 1.3 66.6 + - - +
114G GLN* 3.1 20.2 + - - +
119G VAL* 3.9 21.2 - - + +
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Residues in contact with TYR 112 (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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50G LEU* 3.1 44.3 - - + +
54G MET* 5.9 2.3 - - - -
75G ILE* 4.9 5.7 - - + +
76G ASP* 5.0 4.3 + - - +
77G ARG* 3.3 70.0 - - + +
108G ARG* 3.1 18.3 + - - +
109G GLU 3.1 6.3 + - - +
111G GLU* 1.3 79.1 - - - +
113G PHE* 1.3 80.6 + + - +
114G GLN* 3.3 6.2 + - - +
91H ASP* 4.8 0.7 - - - -
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Residues in contact with PHE 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G SER* 3.6 4.5 - - - -
50G LEU* 2.9 30.3 + - + -
51G LEU* 3.6 39.0 + - + -
54G MET* 6.1 0.7 - - - -
75G ILE* 4.2 14.1 - - + -
77G ARG* 4.4 4.0 - - + -
82G PHE* 3.4 36.6 - + + -
85G ILE* 3.9 20.6 - - + -
109G GLU* 2.8 45.6 + - + +
110G ALA 4.0 3.4 - - - +
112G TYR* 1.3 96.4 - + - +
114G GLN* 1.3 66.5 + - - +
115G LEU* 3.5 17.4 - - + +
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Residues in contact with GLN 114 (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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48G HIS 4.3 7.5 + - - +
49G SER* 3.2 20.6 - - - -
50G LEU* 3.4 26.5 + - - +
53G LYS* 3.3 30.3 + - - +
110G ALA 2.8 9.0 + - - -
111G GLU* 3.1 16.9 + - - +
112G TYR 3.8 6.3 - - - +
113G PHE* 1.3 79.3 - - - +
115G LEU* 1.3 57.1 + - - +
116G PRO* 3.4 13.0 - - + +
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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