Contacts of the helix formed by residues 13 - 21 (chain G) in PDB entry 5UQ9
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 VAL 13 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G LEU 3.7 2.2 - - - -
12G ALA* 1.3 76.0 - - - +
14G MET* 1.3 63.4 + - - +
15G GLY 3.6 0.4 - - - -
16G GLN* 3.6 26.3 + - - +
17G ASN* 3.0 32.1 + - - +
132G GLU* 3.1 34.5 - - - +
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Residues in contact with MET 14 (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* 2.6 17.1 + - + +
13G VAL* 1.3 77.0 - - - +
15G GLY* 1.3 60.9 - - - +
17G ASN* 3.3 1.9 + - + +
18G LEU* 3.1 19.3 + - + +
74G LEU* 4.0 29.4 - - + +
76G LYS* 3.2 33.0 - - + +
128G VAL* 4.5 15.9 - - + -
131G GLY* 3.2 34.8 - - - +
132G GLU* 5.0 5.2 - - - +
135G ALA* 3.8 17.7 - - + -
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Residues in contact with GLY 15 (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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8G LEU* 3.7 5.8 - - - -
10G GLY 3.1 25.8 + - - -
12G ALA 4.6 1.2 - - - +
14G MET* 1.3 76.4 - - - +
16G GLN* 1.3 58.3 + - - +
17G ASN 3.4 0.2 - - - -
18G LEU* 3.7 3.5 - - - +
19G ILE* 2.8 36.9 + - - +
74G LEU* 3.7 19.9 + - - +
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Residues in contact with GLN 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLY 3.8 3.4 + - - -
11G LEU* 4.4 14.1 + - + +
13G VAL* 3.5 36.3 + - - +
14G MET 3.1 0.6 - - - -
15G GLY* 1.3 76.3 - - - +
17G ASN* 1.3 64.6 + - - +
19G ILE* 3.9 1.6 - - - +
20G LEU* 3.1 33.5 + - + +
38G LYS* 3.2 35.8 + - - +
42G PHE* 3.2 45.5 - - + +
46G GLU* 3.5 19.0 - - + +
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Residues in contact with ASN 17 (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 VAL* 3.0 17.5 + - - +
14G MET* 3.9 3.1 - - - +
16G GLN* 1.3 77.8 - - - +
18G LEU* 1.3 65.1 + - - +
20G LEU* 4.6 5.6 - - - +
21G ASN* 3.0 31.5 + - - +
131G GLY 5.3 0.2 - - - +
132G GLU* 2.3 40.2 + - - +
135G ALA* 3.2 21.7 - - + +
136G ARG* 3.1 42.2 + - + +
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Residues in contact with LEU 18 (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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8G LEU* 3.8 17.3 - - + -
14G MET* 3.1 17.3 + - + +
15G GLY* 3.9 5.6 - - - +
16G GLN 3.3 0.2 - - - -
17G ASN* 1.3 76.3 - - - +
19G ILE* 1.3 58.0 + - - +
21G ASN* 4.0 1.5 - - - -
22G MET* 3.2 41.5 + - + +
72G ILE* 5.0 8.5 - - + -
74G LEU* 3.8 22.0 - - + -
128G VAL* 5.4 12.1 - - + -
135G ALA* 3.8 11.8 + - + +
139G PRO* 4.4 23.1 - - + -
141G LEU* 5.7 4.7 - - + -
157G PHE* 6.2 2.0 - - + -
160G ILE* 4.1 20.2 - - + -
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Residues in contact with ILE 19 (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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8G LEU* 3.8 32.3 - - + -
11G LEU* 3.7 16.4 - - + -
15G GLY 2.8 20.4 + - - +
16G GLN 3.9 2.7 - - - +
18G LEU* 1.3 76.2 - - - +
20G LEU* 1.3 67.6 + - - +
22G MET* 3.2 19.0 + - - +
23G ASN* 3.8 6.2 - - - +
29G VAL* 3.6 26.6 - - + +
31G ALA* 3.7 27.1 - - + -
42G PHE* 3.6 24.0 - - + -
52G VAL* 4.0 14.2 - - + +
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Residues in contact with LEU 20 (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 GLN* 3.1 30.8 + - + +
17G ASN* 3.5 5.1 + - - +
19G ILE* 1.3 79.9 - - + +
21G ASN* 1.3 70.1 + - - +
22G MET 3.5 1.6 + - - -
23G ASN* 3.5 21.3 + - - +
42G PHE* 3.4 31.6 - - + -
46G GLU* 4.3 11.2 - - + +
47G ALA* 3.5 26.2 - - + +
52G VAL* 5.7 3.8 - - + -
136G ARG* 5.3 9.4 - - - +
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Residues in contact with ASN 21 (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 ASN 3.0 21.4 + - - +
18G LEU* 4.0 3.1 - - - -
20G LEU* 1.3 83.6 + - - +
22G MET* 1.3 57.3 + - - +
23G ASN* 3.0 7.6 - - - +
24G ASP* 2.9 30.1 - - - +
135G ALA 4.5 1.1 - - - +
136G ARG* 2.7 65.4 + - - +
137G TYR* 4.3 5.7 - - - +
160G ILE* 4.0 2.5 - - - +
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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