Contacts of the strand formed by residues 34 - 42 (chain H) 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 34 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G VAL* 4.2 9.0 - - + -
14G TYR 3.5 2.5 - - - +
15G GLN* 3.4 34.3 - - + +
71G LEU* 4.6 3.3 - - - +
83G ALA* 4.7 4.5 - - + +
114G PHE* 4.6 9.4 - - + -
115G PRO* 3.7 19.1 - - + -
116G PRO* 4.0 13.9 - - + -
146G PHE* 5.1 4.0 - - + -
33H PHE* 1.3 81.2 - - - +
35H TYR* 1.3 71.9 + - - +
36H GLN* 5.4 2.5 - - + +
57H ILE 3.9 0.2 - - - +
58H TYR* 4.0 2.3 - - - -
59H ASN* 2.6 54.1 + - - +
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Residues in contact with TYR 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G SER 4.3 0.2 - - - -
13G VAL* 3.3 8.0 - - - +
14G TYR 2.8 34.6 + - - +
67G VAL* 3.3 35.2 - - + -
70G ASN* 3.8 27.2 + - + -
71G LEU* 3.9 34.0 - - + +
74G LEU* 4.2 5.8 - - + -
34H VAL* 1.3 75.5 - - - +
36H GLN* 1.3 86.4 + - - +
37H PHE* 4.5 9.2 - - + -
56H TYR* 3.0 18.7 - + + +
57H ILE 3.6 8.5 - - - -
58H TYR* 4.7 4.3 - - - -
63H TYR* 2.6 49.0 + + - -
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Residues in contact with GLN 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ILE* 4.7 2.6 - - + +
12G SER 3.3 4.3 - - - +
13G VAL* 4.5 10.3 - - + -
114G PHE* 5.8 0.4 - - - -
140G VAL* 3.7 14.6 - - - +
144G TYR* 3.8 26.9 + - - +
145G SER 5.3 0.4 + - - -
146G PHE* 3.3 34.0 - - + -
34H VAL* 5.4 3.1 - - + +
35H TYR* 1.3 83.8 - - - +
37H PHE* 1.3 69.2 + - - +
38H MET* 2.9 30.6 - - - +
55H ARG 3.6 1.7 - - - +
56H TYR* 3.4 3.6 - - - -
57H ILE* 2.8 48.9 + - + +
59H ASN 5.7 2.9 + - - +
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Residues in contact with PHE 37 (chain H).
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 3.5 14.6 - - - -
11G ILE* 3.1 6.4 - - - +
12G SER* 2.6 46.3 + - - +
63G ASN* 3.5 11.9 - - - -
67G VAL* 4.4 8.5 - - + -
6H ALA* 3.7 25.4 - - + -
7H LYS 3.2 26.7 - - - -
8H ALA* 3.8 7.4 - - + -
35H TYR* 4.5 7.6 - - + -
36H GLN* 1.3 76.0 - - - +
38H MET* 1.3 69.0 + - - +
54H THR* 3.7 25.1 - - + -
55H ARG 3.4 13.0 - - - -
56H TYR* 3.3 42.8 - + - -
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Residues in contact with MET 38 (chain H).
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* 4.3 16.2 - - + -
9G TYR 3.8 4.5 - - - -
11G ILE* 4.1 13.2 - - + +
140G VAL* 3.5 24.7 - - + -
141G ASN 5.5 0.2 - - - +
144G TYR* 4.4 19.3 - - + -
36H GLN* 2.9 30.3 - - + +
37H PHE* 1.3 87.5 - - - +
39H GLY* 1.3 59.8 + - - +
40H GLU* 2.8 36.6 + - - +
53H VAL 3.7 1.2 - - - +
54H THR* 3.6 4.0 - - - +
55H ARG* 3.4 35.0 + - + +
57H ILE* 4.6 0.9 - - + -
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Residues in contact with GLY 39 (chain H).
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 3.7 2.1 - - - +
9G TYR* 2.6 35.9 + - - +
6H ALA* 3.7 22.2 - - - +
38H MET* 1.3 70.9 - - - +
40H GLU* 1.3 63.3 + - - +
41H CYS* 3.4 6.1 + - - -
52H TYR* 3.7 18.5 - - - -
53H VAL 4.1 0.2 - - - -
54H THR* 4.1 7.6 - - - -
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Residues in contact with GLU 40 (chain H).
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* 5.1 4.5 - - + -
7G GLY 3.5 7.6 - - - +
8G THR* 4.2 17.4 - - + +
9G TYR 4.5 0.4 - - - +
38H MET* 2.8 31.5 + - + +
39H GLY* 1.3 73.8 - - - +
41H CYS* 1.3 58.8 + - - +
42H TYR* 2.4 37.0 + - + +
52H TYR* 4.2 0.2 - - - -
53H VAL 2.8 43.9 + - - +
55H ARG* 2.3 38.3 + - - -
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Residues in contact with CYS 41 (chain H).
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* 4.7 1.1 - - - +
7G GLY 3.0 22.8 + - - -
9G TYR* 4.0 7.6 - - - -
39H GLY 3.8 5.2 - - - -
40H GLU* 1.3 71.7 - - - +
42H TYR* 1.3 58.7 + - - +
43H PHE* 3.1 28.1 - - - -
50H ILE* 4.6 0.4 - - + -
51H ARG 3.1 10.8 - - - +
52H TYR* 3.1 28.7 - - + -
104H VAL 3.8 6.7 - - - -
105H CYS* 2.0 48.2 - - - -
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Residues in contact with TYR 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G ILE* 3.2 49.4 + - + +
2G GLU 5.2 0.4 - - - +
3G ALA* 3.6 15.7 - - + -
5G HIS 4.1 3.1 - - - -
6G VAL* 3.9 21.8 - - + -
40H GLU* 2.4 57.3 + - + -
41H CYS* 1.3 71.1 - - - +
43H PHE* 1.3 61.5 + - - +
49H ARG 3.4 3.1 - - - +
50H ILE* 3.1 7.7 - - - -
51H ARG* 2.7 60.2 + - + +
53H VAL* 4.3 11.0 - - + -
55H ARG* 4.1 3.6 + - - -
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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