Contacts of the strand formed by residues 3 - 16 (chain A) in PDB entry 2L1B
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 GLN 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GLY 4.8 1.2 - - - +
2A GLU* 1.3 80.6 - - - +
4A VAL* 1.3 62.8 + - - +
5A PHE* 3.6 28.5 + - + -
26A TRP* 4.3 0.7 - - - -
26B ARG* 3.4 2.3 - - - -
27B M3L 2.9 66.7 + - + +
29B ALA* 5.3 6.7 - - - +
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Residues in contact with VAL 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLU* 3.0 35.2 + - + +
3A GLN* 1.3 69.7 - - - +
5A PHE* 1.3 74.3 + - - +
43A LEU* 3.6 27.8 - - + -
24B ALA* 4.7 7.4 - - + -
25B ALA 3.5 6.7 - - - +
26B ARG* 3.9 16.8 - - + +
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Residues in contact with PHE 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLN* 3.6 32.1 + - + -
4A VAL* 1.3 77.0 - - - +
6A ALA* 1.3 64.8 + - - +
26A TRP* 3.3 19.6 - - + -
29A TRP* 3.5 37.7 - + + +
24B ALA* 3.6 5.4 - - - +
25B ALA 3.0 29.8 + - - +
27B M3L 3.6 31.2 - - - -
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 1.3 74.4 - - - +
7A VAL* 1.3 58.6 + - - +
26A TRP* 3.8 7.0 - - - +
27A LYS* 3.1 46.8 + - - +
28A GLY 4.0 4.4 + - - +
29A TRP* 5.3 0.5 - - - -
23B LYS 3.7 11.0 - - - +
24B ALA* 4.3 4.5 - - + +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 1.3 74.2 - - - +
8A GLU* 1.3 61.1 + - - +
9A SER 3.4 17.7 - - - +
10A ILE* 5.4 0.2 - - + -
24A VAL* 3.5 19.1 - - + -
25A LYS 3.2 18.6 - - - +
26A TRP* 3.9 13.2 - - + +
27A LYS* 3.7 11.5 - - - +
47A LEU* 3.5 25.4 - - + -
21B ALA 4.3 9.4 - - - +
23B LYS* 3.1 22.1 + - - +
24B ALA 3.7 0.7 - - - -
25B ALA* 3.4 27.6 - - + +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 1.3 73.9 - - - +
9A SER* 1.4 74.2 + - - +
25A LYS* 2.9 53.6 + - - +
26A TRP 3.9 0.7 - - - -
27A LYS* 3.2 27.4 - - + +
47A LEU* 4.5 4.5 - - - +
19B GLN 5.1 5.9 - - - +
20B LEU* 6.1 5.4 - - + -
21B ALA* 5.0 8.3 + - - +
23B LYS* 5.8 0.3 - - - +
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Residues in contact with SER 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.4 9.0 - - - +
8A GLU* 1.4 98.5 + - - +
10A ILE* 1.3 72.6 + - - +
11A ARG* 5.5 0.3 - - - -
24A VAL* 3.9 0.9 - - - -
25A LYS* 2.9 28.3 + - - +
47A LEU* 4.0 13.7 - - - -
50A ALA* 6.5 0.9 - - - -
51A TYR* 6.1 1.8 - - - -
19B GLN* 5.8 6.7 - - - -
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Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER* 1.3 81.4 + - - +
11A ARG* 1.3 58.9 + - - +
12A LYS 3.1 29.2 - - - +
22A TYR* 3.8 32.1 - - + -
23A LEU 3.6 3.8 - - - +
24A VAL* 4.1 24.9 - - + -
42A ILE* 5.0 3.6 - - + -
47A LEU* 3.7 38.9 + - + -
48A VAL* 3.8 7.9 - - + +
51A TYR* 3.1 43.9 - - + +
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Residues in contact with ARG 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER* 3.9 3.2 + - - -
10A ILE* 1.3 73.4 - - - +
12A LYS* 1.4 83.2 + - - +
23A LEU* 2.8 30.8 + - + +
25A LYS* 3.9 25.1 - - + +
31A PRO* 5.3 11.6 - - + +
34A SER* 5.4 1.3 - - - +
51A TYR* 3.6 12.3 + - - -
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Residues in contact with LYS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 3.1 14.7 - - - +
11A ARG* 1.4 105.9 - - - +
13A LYS* 1.3 62.8 + - - +
22A TYR* 3.6 0.3 - - - -
23A LEU* 2.9 39.6 + - + +
36A TRP* 3.8 26.4 - - + -
51A TYR* 3.8 7.9 - - - -
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Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LYS* 1.3 79.3 - - - +
14A ARG* 1.3 71.5 + - - +
15A VAL* 5.8 2.7 - - - -
20A VAL* 3.7 23.4 - - - +
21A GLU 3.4 7.4 - - - +
22A TYR* 3.8 26.6 + - + -
36A TRP* 4.6 2.0 - - - -
48A VAL* 4.6 1.3 - - + -
51A TYR* 3.7 22.9 + - + +
52A GLU* 2.8 43.3 + - - +
55A GLU* 6.5 0.4 - - + -
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Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 1.3 78.5 - - - +
15A VAL* 1.3 69.4 + - - +
16A ARG* 3.0 43.1 - - - +
20A VAL* 3.4 7.8 - - - +
21A GLU* 2.9 60.5 + - + +
36A TRP* 3.5 39.0 - - + -
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 5.8 2.7 - - - -
14A ARG* 1.3 85.3 + - - +
16A ARG* 1.3 64.6 + - - +
18A GLY* 3.9 26.0 - - - +
19A LYS 3.4 10.3 - - - +
20A VAL* 4.0 21.5 - - + -
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Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.0 31.9 - - - +
15A VAL* 1.3 73.3 - - - +
17A LYS* 1.4 74.6 + - + +
18A GLY 3.1 1.1 - - - -
19A LYS* 3.0 29.5 + - - +
21A GLU* 3.1 39.1 + - - +
36A TRP* 4.5 17.4 - - - +
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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