Contacts of the helix formed by residues 102 - 118 (chain G) in PDB entry 4UN7
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 ASN 102 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8G SER* 5.3 4.2 + - - -
100G LEU 3.4 3.6 + - - +
101G PHE* 1.3 75.3 - - - +
103G MET* 1.3 61.0 + - - +
104G ARG* 3.2 15.5 + - - +
105G GLU* 2.7 45.7 + - - +
106G GLN* 2.8 30.0 + - - +
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Residues in contact with MET 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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102G ASN* 1.3 76.3 - - - +
104G ARG* 1.3 63.1 + - - +
106G GLN* 3.7 14.7 - - - +
107G ILE* 3.2 41.6 + - + +
145G LEU* 3.7 29.8 - - + -
176G THR* 5.8 2.7 - - + -
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Residues in contact with ARG 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G GLU* 3.4 38.4 + - - +
6G GLU* 5.5 0.9 - - - +
8G SER* 5.1 2.0 - - - -
9G GLY* 4.3 14.8 - - - -
102G ASN* 3.2 15.3 + - - +
103G MET* 1.3 78.2 - - - +
105G GLU* 1.3 60.2 + - + +
107G ILE* 3.4 8.2 + - - +
108G ALA* 3.1 26.5 + - + +
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Residues in contact with GLU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G SER* 3.5 41.1 - - - +
9G GLY* 4.8 0.9 - - - +
12G ALA* 3.5 12.2 - - + +
94G MET* 4.2 8.4 - - + +
100G LEU 4.5 0.3 - - - +
101G PHE* 3.2 29.7 - - + -
102G ASN* 2.7 44.6 + - - +
104G ARG* 1.3 77.0 - - + +
106G GLN* 1.3 59.7 + - - +
108G ALA* 4.6 0.7 - - - -
109G PHE* 2.8 32.7 + - - +
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Residues in contact with GLN 106 (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 ARG 5.7 0.6 + - - -
101G PHE* 3.0 24.7 + - + -
102G ASN* 2.8 21.5 + - - +
103G MET* 3.7 12.6 - - - +
105G GLU* 1.3 75.6 - - - +
107G ILE* 1.3 66.5 + - + +
109G PHE* 3.7 0.9 - - - +
110G ILE* 3.0 32.5 + - + +
141G TRP* 3.4 66.6 - - + +
144G ASN* 6.2 0.2 - - - +
145G LEU* 4.8 10.4 - - + +
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Residues in contact with ILE 107 (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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103G MET* 3.2 42.7 + - + +
104G ARG* 3.8 6.3 - - - +
105G GLU 3.2 0.2 - - - -
106G GLN* 1.3 79.0 - - + +
108G ALA* 1.3 58.0 + - - +
110G ILE* 3.8 1.7 - - - +
111G LYS* 2.9 28.6 + - - +
145G LEU* 4.4 11.4 - - + -
176G THR* 3.6 34.1 - - + +
177G ILE* 4.1 25.1 - - + +
180G SER* 3.8 20.0 - - - +
181G HIS* 5.8 0.2 - - + -
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Residues in contact with ALA 108 (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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9G GLY* 3.2 30.3 - - - +
12G ALA* 4.0 2.5 - - + -
13G TYR* 3.6 13.9 - - + +
104G ARG* 3.1 16.8 + - + +
105G GLU 3.9 2.7 - - - +
106G GLN 3.3 0.2 - - - -
107G ILE* 1.3 77.7 - - - +
109G PHE* 1.3 56.7 + - - +
111G LYS* 3.1 5.1 + - - +
112G GLY 2.8 25.8 + - - -
181G HIS* 3.8 25.4 - - + +
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Residues in contact with PHE 109 (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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12G ALA 3.4 22.1 + - - +
15G LEU* 3.9 20.9 - - + -
16G GLY* 3.7 23.3 - - - -
19G ILE* 4.0 13.5 - - + -
98G ILE* 3.8 20.0 - - + -
101G PHE* 4.0 20.4 - + + -
105G GLU 2.8 18.6 + - - +
106G GLN 3.7 3.1 - - - +
108G ALA* 1.3 76.8 - - - +
110G ILE* 1.3 54.9 + - - +
112G GLY* 3.0 2.8 + - - -
113G LEU* 2.7 45.0 + - + +
134G LEU* 4.0 22.4 - - + -
138G VAL* 4.2 13.7 - - + -
141G TRP* 3.6 19.1 - + + -
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Residues in contact with ILE 110 (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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106G GLN* 3.0 21.1 + - + +
107G ILE 3.8 3.1 - - - +
109G PHE* 1.3 72.3 - - + +
111G LYS* 1.3 60.2 + - - +
113G LEU* 3.7 7.2 - - - +
114G TYR* 2.8 28.6 + - - +
127G ILE* 4.8 13.2 - - + +
138G VAL* 4.2 18.6 - - + -
141G TRP* 3.8 37.7 - - + -
142G LEU* 4.1 19.3 - - + -
145G LEU* 4.9 2.9 - - + -
173G PHE* 4.4 14.8 - - + -
177G ILE* 3.5 26.7 - - + -
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Residues in contact with LYS 111 (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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13G TYR* 4.0 15.7 - - + -
107G ILE 2.9 13.6 + - - +
108G ALA* 3.4 9.0 - - - +
110G ILE* 1.3 76.9 - - - +
112G GLY* 1.3 57.2 + - - +
114G TYR* 3.2 4.8 + - - +
115G VAL* 2.8 42.6 + - + +
177G ILE* 3.4 25.9 - - - +
178G LEU* 3.2 27.6 + - + +
180G SER* 3.0 36.9 + - - +
181G HIS* 3.4 26.9 - - + +
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Residues in contact with GLY 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 3.6 36.3 - - - -
16G GLY 3.8 7.3 - - - -
17G LEU* 3.4 13.7 - - - +
108G ALA 2.8 10.7 + - - -
109G PHE 3.5 2.9 - - - -
111G LYS* 1.3 75.5 - - - +
113G LEU* 1.3 62.8 + - - +
115G VAL 3.4 0.9 + - - -
116G ALA* 3.1 19.8 + - - +
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Residues in contact with LEU 113 (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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16G GLY* 3.7 12.6 - - - +
19G ILE* 4.3 13.7 - - + -
20G GLY* 4.1 13.5 - - - +
109G PHE* 2.7 30.3 + - + +
110G ILE* 3.9 6.3 - - - +
112G GLY* 1.3 72.3 - - - +
114G TYR* 1.3 52.7 + - - +
116G ALA* 3.4 0.8 + - - +
117G GLU* 2.6 59.6 + - + +
127G ILE* 3.9 28.7 - - + +
129G ASN* 4.8 4.0 - - - +
134G LEU* 4.7 6.7 - - + -
135G LEU* 4.6 9.2 - - + -
138G VAL* 4.2 25.4 - - + -
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Residues in contact with TYR 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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110G ILE 2.8 21.4 + - - +
111G LYS 3.7 3.4 - - - +
113G LEU* 1.3 73.0 - - - +
115G VAL* 1.3 64.9 + - - +
118G GLY* 2.8 31.9 + - - +
119G ASP 2.8 38.0 + - - -
120G LYS* 3.7 7.4 - - + -
122G LEU* 4.3 11.4 - - + -
125G LEU* 3.4 27.3 - - + +
126G ARG 3.4 9.4 + - - -
127G ILE* 3.4 34.9 - - + +
165G ILE* 4.3 3.8 - - + -
173G PHE* 3.7 27.1 - + + -
178G LEU* 3.8 25.6 - - + -
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Residues in contact with VAL 115 (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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13G TYR* 4.0 19.3 - - + +
17G LEU* 3.9 17.9 - - + -
21G ASP* 4.8 0.5 - - - +
42G GLN* 5.1 6.4 + - - +
47G LEU* 4.8 21.4 - - + +
51G HIS* 5.8 0.7 - - + -
52G ILE* 6.5 0.2 - - + -
111G LYS* 2.8 30.6 + - + +
112G GLY 3.4 5.4 + - - +
114G TYR* 1.3 75.4 - - - +
116G ALA* 1.3 57.6 + - - +
120G LYS* 3.0 25.2 + - - +
178G LEU* 5.6 4.0 - - + -
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Residues in contact with ALA 116 (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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17G LEU* 4.3 10.5 - - + +
20G GLY* 3.8 20.4 - - - -
21G ASP* 3.3 31.9 - - + +
42G GLN* 5.2 0.4 - - - +
112G GLY 3.1 15.2 + - - +
113G LEU 3.9 1.1 - - - +
114G TYR 3.1 0.6 - - - -
115G VAL* 1.3 78.6 - - - +
117G GLU* 1.3 61.0 + - - +
118G GLY 3.6 0.4 - - - -
120G LYS* 3.7 7.2 + - - -
1182G ZN 2.4 26.4 - - - -
16I C 3.1 3.5 + - - +
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Residues in contact with GLU 117 (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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20G GLY* 3.1 39.0 - - - +
113G LEU* 2.6 27.2 + - + +
116G ALA* 1.3 71.5 - - - +
118G GLY* 1.3 59.6 + - - +
127G ILE* 3.9 8.5 - - + -
128G TRP* 3.1 48.9 + - - +
129G ASN* 2.8 21.3 + - - -
15I C 2.5 50.8 + - - +
16I C 3.9 9.1 + - - +
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Residues in contact with GLY 118 (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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113G LEU 3.8 0.2 + - - -
114G TYR* 2.8 36.2 + - - -
116G ALA 3.6 1.0 - - - -
117G GLU* 1.3 80.7 - - - +
119G ASP* 1.3 62.2 + - - -
120G LYS* 3.1 21.4 + - - -
126G ARG 3.2 9.4 - - - -
127G ILE* 4.4 0.7 - - - -
128G TRP* 4.0 2.5 - - - -
16I C 3.8 10.0 - - - +
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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