Contacts of the strand formed by residues 34 - 42 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C VAL* 3.8 19.1 - - + -
14C TYR 3.5 3.6 - - - +
15C GLN* 3.0 35.7 - - + +
71C LEU* 4.4 4.0 - - - +
83C ALA* 4.7 2.4 - - + +
114C PHE* 4.2 24.7 - - + -
115C PRO* 3.8 9.6 - - + -
116C PRO* 3.7 14.6 - - + -
146C PHE* 5.1 4.3 - - + -
33D PHE* 1.3 77.5 - - - +
35D TYR* 1.3 71.7 + - - +
36D GLN* 5.3 2.5 - - + +
57D ILE 3.9 0.2 - - - +
58D TYR* 4.0 2.4 - - - -
59D ASN* 2.6 42.1 + - - +
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Residues in contact with TYR 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C VAL* 3.3 9.5 - - - +
14C TYR* 2.9 31.9 + - + +
67C VAL* 3.1 38.8 - - + -
70C ASN* 2.9 46.4 + - + -
71C LEU* 3.6 32.7 - - + +
74C LEU* 4.2 5.6 - - + -
34D VAL* 1.3 74.3 - - - +
36D GLN* 1.3 75.7 + - - +
37D PHE* 5.0 2.9 - - + -
56D TYR* 3.6 16.5 - + + -
57D ILE 3.6 7.6 - - - -
58D TYR* 4.7 5.8 - + - -
63D TYR* 2.6 41.4 + + - -
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Residues in contact with GLN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.8 3.7 - - + +
12C SER 3.3 3.4 - - - -
13C VAL* 4.0 11.7 - - + -
114C PHE* 5.8 0.4 - - - -
140C VAL* 3.4 28.9 - - - +
144C TYR* 4.0 19.9 + - - +
146C PHE* 3.1 35.0 - - - -
34D VAL* 5.3 3.0 - - + +
35D TYR* 1.3 83.8 - - - +
37D PHE* 1.3 70.5 + - - +
38D MET* 4.2 10.0 - - - +
55D ARG 3.5 1.4 - - - +
56D TYR* 3.4 4.2 - - - -
57D ILE* 2.8 58.7 + - + +
59D ASN 5.7 2.0 + - - +
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Residues in contact with PHE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C GLY 3.5 14.6 - - - -
11C ILE* 3.1 5.7 - - - +
12C SER* 2.6 44.6 + - - +
63C ASN* 3.8 10.1 - - - -
67C VAL* 4.7 4.3 - - + -
6D ALA* 3.7 30.7 - - + -
7D LYS 3.2 20.2 - - - -
8D ALA* 3.9 10.5 - - + -
35D TYR* 4.8 3.6 - - + -
36D GLN* 1.3 76.6 - - - +
38D MET* 1.3 79.1 + - - +
54D THR* 3.6 32.1 - - + -
55D ARG 3.5 10.8 - - - -
56D TYR* 3.5 42.6 - + + -
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Residues in contact with MET 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C THR* 4.5 14.4 - - + -
9C TYR 3.8 5.6 - - - -
11C ILE* 4.1 16.2 - - + +
140C VAL* 4.0 26.0 - - + -
141C ASN 5.7 0.4 - - - +
144C TYR* 4.3 7.9 - - + -
36D GLN* 4.2 6.7 - - - +
37D PHE* 1.3 86.2 - - - +
39D GLY* 1.3 59.3 + - - +
40D GLU* 2.9 34.7 + - - +
54D THR* 3.5 4.3 - - - +
55D ARG* 3.4 46.4 + - + +
57D ILE* 4.0 16.4 - - - -
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Residues in contact with GLY 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C GLY 3.7 1.9 - - - +
9C TYR* 2.6 35.3 + - - +
6D ALA* 3.7 19.4 - - - +
37D PHE* 4.0 3.0 - - - -
38D MET* 1.3 71.2 - - - +
40D GLU* 1.3 64.1 + - - +
41D CYS* 3.4 7.4 + - - -
52D TYR* 3.4 20.0 - - - -
54D THR* 4.0 4.5 - - - -
104D VAL 5.2 0.2 - - - +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 5.1 4.3 - - + -
7C GLY 3.4 8.7 - - - +
8C THR* 4.1 18.3 - - + +
9C TYR 4.4 0.8 - - - +
38D MET* 2.9 31.9 + - + +
39D GLY* 1.3 73.8 - - - +
41D CYS* 1.3 58.7 + - - +
42D TYR* 2.4 38.8 + - + -
53D VAL* 2.8 40.4 + - + +
55D ARG* 2.5 34.6 + - - -
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Residues in contact with CYS 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C VAL* 5.0 1.1 - - - +
7C GLY 3.1 17.4 + - - +
9C TYR* 4.0 7.4 - - - -
39D GLY 3.8 11.0 - - - -
40D GLU* 1.3 70.9 - - - +
42D TYR* 1.3 63.4 + - - +
43D PHE* 3.4 17.5 - - - -
50D ILE* 4.6 0.2 - - + -
51D ARG 3.0 10.8 - - - +
52D TYR* 3.0 27.1 - - + -
104D VAL 3.9 4.7 - - - -
105D CYS* 2.0 50.2 - - + -
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Residues in contact with TYR 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ILE* 3.0 53.4 + - + +
2C GLU 5.2 0.4 - - - +
3C ALA* 3.6 15.5 - - + -
5C HIS 4.1 3.4 - - - -
6C VAL* 4.2 20.2 - - + +
40D GLU* 2.4 53.7 + - + -
41D CYS* 1.3 71.4 - - - +
43D PHE* 1.3 60.8 + - - +
44D THR* 5.5 0.2 - - - -
49D ARG 3.4 2.9 - - - +
50D ILE* 3.1 7.8 - - - -
51D ARG* 2.6 59.5 + - + +
53D VAL* 4.3 11.9 - - + -
55D ARG* 3.7 6.6 + - - -
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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