Contacts of the strand formed by residues 6 - 15 (chain G) in PDB entry 1LNU
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 6 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3G ALA* 5.6 1.8 - - + +
4G ASP 3.8 3.1 + - - +
5G HIS* 1.3 74.7 - - - +
7G GLY* 1.3 69.2 + - - +
8G THR* 3.8 11.0 + - - +
27G PHE* 2.9 20.0 - - - -
28G ASP* 3.1 31.2 + - - +
29G GLY 5.2 1.3 - - - +
40H GLU* 5.1 3.4 - - + -
41H CYS 4.4 4.5 - - - +
42H TYR* 3.9 37.7 - - + -
43H PHE* 4.0 1.3 - - - -
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Residues in contact with GLY 7 (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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6G VAL* 1.3 75.7 - - - +
8G THR* 1.3 61.4 + - - -
9G TYR* 3.3 40.3 - - - -
27G PHE* 3.6 5.8 - - - -
40H GLU* 3.5 0.5 - - - -
41H CYS 3.0 27.3 + - - +
43H PHE* 3.2 13.8 - - - -
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Residues in contact with THR 8 (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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6G VAL* 3.8 14.9 + - - +
7G GLY* 1.3 70.1 - - - -
9G TYR* 1.3 64.2 + - - +
11G ILE* 3.5 24.5 - - + -
26G GLU* 2.6 61.9 + - - +
27G PHE* 5.2 0.3 - - - -
28G ASP 5.5 0.3 + - - -
29G GLY 5.9 0.3 + - - -
140G VAL* 4.9 4.3 - - + -
38H MET* 4.3 20.4 - - + -
40H GLU* 4.2 20.3 - - + +
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Residues in contact with TYR 9 (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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7G GLY* 3.3 36.3 - - - -
8G THR* 1.3 80.7 - - - +
10G GLY* 1.3 62.6 + - - +
11G ILE* 3.0 4.5 + - - +
25G PHE* 3.0 36.8 - + + +
26G GLU 4.0 1.3 - - - -
27G PHE* 3.9 2.3 - - - -
32G LEU* 3.8 13.2 - - + -
4H GLN 4.7 2.5 - - - +
6H ALA* 4.5 7.2 - - + -
38H MET* 3.8 0.5 - - - -
39H GLY* 2.6 42.6 + - - +
41H CYS* 4.0 20.6 - - - -
43H PHE* 4.2 9.1 - + - -
104H VAL* 4.4 6.1 - - + -
105H CYS* 4.7 0.2 - - - -
108H ASN* 3.7 28.5 - - + +
113H GLU* 2.9 40.0 + - - +
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Residues in contact with GLY 10 (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 TYR* 1.3 71.7 - - - +
11G ILE* 1.3 66.4 + - - +
12G SER* 2.9 16.8 + - - -
23G TYR* 3.0 27.1 - - - -
24G THR 3.8 0.2 - - - -
25G PHE* 3.0 18.1 - - - -
63G ASN* 3.8 0.7 + - - -
6H ALA* 4.3 13.2 - - - -
37H PHE* 3.5 15.7 - - - -
38H MET* 4.5 0.2 - - - -
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Residues in contact with ILE 11 (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 THR* 3.5 33.0 - - + +
9G TYR 3.0 7.1 + - - +
10G GLY* 1.3 72.7 - - - +
12G SER* 1.3 59.2 + - - +
13G VAL* 4.1 15.2 - - + +
22G GLN 3.5 1.6 - - - +
23G TYR* 3.3 5.9 - - - -
24G THR* 2.8 56.3 + - - +
26G GLU* 3.1 37.2 - - + +
140G VAL* 3.6 18.6 - - + -
146G PHE* 5.8 0.4 - - + -
36H GLN* 4.7 4.9 - - - +
37H PHE 3.1 13.0 - - - +
38H MET* 4.1 7.9 - - + +
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Residues in contact with SER 12 (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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10G GLY 2.9 7.0 + - - -
11G ILE* 1.3 70.8 - - - +
13G VAL* 1.3 62.1 + - - +
22G GLN 3.7 3.8 - - - -
23G TYR* 3.2 15.8 - - - -
63G ASN* 2.6 27.3 + - - +
64G ILE* 4.5 5.4 - - - -
67G VAL* 3.1 31.1 - - - +
35H TYR 3.8 0.7 - - - +
36H GLN* 3.3 2.9 - - - -
37H PHE* 2.6 39.3 + - - -
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Residues in contact with VAL 13 (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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11G ILE* 4.7 10.1 - - + -
12G SER* 1.3 78.4 - - - +
14G TYR* 1.3 70.5 + - - +
15G GLN* 4.7 2.9 - - - +
20G ILE 5.3 1.1 - - - +
21G GLY* 3.3 3.5 - - - -
22G GLN* 3.0 52.0 + - + +
64G ILE* 4.3 4.0 - - - +
67G VAL* 4.2 0.7 - - - -
116G PRO* 4.3 16.2 - - + -
146G PHE* 3.8 29.4 - - + -
34H VAL* 4.2 16.4 - - + -
35H TYR 3.3 11.0 - - - +
36H GLN* 4.5 10.1 - - + -
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Residues in contact with TYR 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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13G VAL* 1.3 76.6 - - - +
15G GLN* 1.3 71.6 + - - +
16G SER* 4.8 4.9 - - - -
19G ASP* 2.6 55.2 + - - +
20G ILE 3.1 17.3 - - - -
21G GLY* 3.9 6.3 - - - -
64G ILE* 4.1 17.0 - - + -
67G VAL* 3.4 21.1 - - + -
68G LYS* 2.7 56.2 - - + +
71G LEU* 3.7 16.0 - - + +
34H VAL* 3.5 2.1 - - - +
35H TYR* 2.8 35.6 + - + +
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Residues in contact with GLN 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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13G VAL* 4.7 3.9 - - + +
14G TYR* 1.3 79.1 - - - +
16G SER* 1.3 68.8 + - - +
17G PRO* 3.5 7.6 - - + +
19G ASP* 3.3 17.5 + - - -
20G ILE* 2.8 37.7 + - + +
71G LEU* 4.1 1.3 - - - -
115G PRO* 3.5 25.3 - - - +
116G PRO* 3.0 34.1 - - - +
117G VAL* 3.3 27.7 - - - +
169G TRP* 5.3 0.8 - - - -
32H HIS* 5.7 3.0 - - - +
33H PHE 3.0 5.4 - - - +
34H VAL* 3.4 23.1 - - + +
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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