Contacts of the strand formed by residues 39 - 48 (chain B) in PDB entry 1I5L
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 ASN 39 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.5 12.0 - - + +
6A LEU* 5.9 2.0 - - - +
38A MET* 4.0 15.4 - - + +
34B TYR* 3.2 22.2 - - - -
35B ASP* 3.1 34.8 + - - +
37B HIS* 3.5 14.0 - - - +
38B MET* 1.3 81.3 - - - +
40B LEU* 1.3 60.3 + - - +
61B VAL* 5.3 0.2 - - + -
62B ILE 3.2 11.9 - - - +
63B ARG* 3.3 6.4 - - - -
64B GLY 2.7 23.3 + - - +
101B URI 3.2 26.7 + - - -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.2 0.4 - - - -
9B LEU* 4.9 9.0 - - + -
19B VAL* 3.8 39.0 - - + -
31B LEU* 4.5 12.8 - - + -
33B GLY 3.9 7.0 - - - +
34B TYR* 4.0 14.1 - - + -
38B MET* 3.2 30.7 - - + +
39B ASN* 1.3 77.6 - - - +
41B VAL* 1.3 69.4 + - - +
42B LEU* 4.2 2.2 - - + -
60B VAL 4.4 0.2 - - - -
61B VAL* 3.3 8.1 - - - +
62B ILE* 3.0 43.4 + - + +
67B VAL* 4.0 13.9 - - + -
70B VAL* 4.1 13.5 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ARG 4.2 3.4 - - - +
5A PRO* 3.3 41.5 - - + -
8A VAL* 3.6 31.4 - - + -
31B LEU* 3.7 4.0 - - - +
32B ASP* 2.7 43.3 + - + +
33B GLY* 3.4 19.1 + - - +
40B LEU* 1.3 78.4 - - - +
42B LEU* 1.3 67.2 + - - +
43B LEU* 5.5 2.0 - - + -
59B SER* 5.5 3.8 - - - -
60B VAL 3.4 7.6 - - - +
61B VAL* 4.8 2.9 - - + -
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.9 26.9 - - + -
19B VAL* 4.0 11.0 - - + -
27B PHE* 3.8 26.5 - - + -
29B GLY 4.2 5.2 - - - +
30B THR 3.3 11.9 - - - +
31B LEU* 3.9 13.5 - - + -
40B LEU* 5.1 2.7 - - + -
41B VAL* 1.3 77.6 - - - +
43B LEU* 1.3 63.3 + - - +
45B ALA* 4.2 12.8 - - + -
59B SER* 3.0 27.4 - - - -
60B VAL* 2.9 25.7 + - + -
62B ILE* 3.7 30.3 - - + -
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 5.8 5.8 - - - +
29B GLY* 3.6 1.0 - - - -
30B THR* 2.9 41.1 + - + +
32B ASP* 3.5 32.8 - - + +
41B VAL* 5.6 2.2 - - + -
42B LEU* 1.3 76.0 - - - +
44B ASP* 1.3 85.4 + - - +
45B ALA 3.3 0.8 + - - -
58B GLY 3.6 13.9 - - - +
59B SER* 3.6 13.7 - - - -
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG 3.7 1.2 - - - +
29B GLY* 3.4 10.2 - - - -
30B THR* 4.2 5.4 + - - +
43B LEU* 1.3 87.3 - - - +
45B ALA* 1.3 58.6 + - - +
46B GLU* 5.2 1.9 - - - +
57B VAL 3.8 6.7 - - - -
58B GLY* 3.0 18.8 + - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.1 19.1 - - + -
28B ARG 3.0 16.2 - - - +
29B GLY* 4.1 4.5 - - - -
42B LEU* 4.2 19.5 - - + -
43B LEU 4.6 0.4 - - - -
44B ASP* 1.3 76.0 - - - +
46B GLU* 1.3 66.5 + - - +
56B LYS* 3.5 5.0 - - - +
57B VAL* 3.0 40.7 + - + +
60B VAL* 4.6 2.2 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLU 3.6 0.2 - - - +
27B PHE* 3.4 10.7 - - - -
28B ARG* 3.1 47.0 + - - +
44B ASP 5.2 2.0 - - - +
45B ALA* 1.3 81.4 - - - +
47B GLU* 1.3 64.3 + - - +
48B ILE* 3.8 11.1 + - + +
53B VAL* 3.2 32.3 - - - +
55B ARG 3.2 19.1 - - - +
56B LYS* 3.4 24.8 + - + +
57B VAL* 5.4 0.4 - - - -
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 3.3 6.2 + - - -
69A PHE* 4.7 7.8 - - - -
25B ARG* 2.5 46.8 + - + +
26B GLU 3.5 8.1 - - - +
27B PHE* 4.3 25.3 - - + -
46B GLU* 1.3 72.2 - - - +
48B ILE* 1.4 68.0 + - - +
49B GLN* 6.3 1.1 - - + -
54B VAL* 3.2 31.7 + - + +
55B ARG* 2.9 48.0 + - + +
56B LYS* 5.3 0.2 - - - +
57B VAL* 5.9 0.8 - - - +
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLY 4.6 2.6 - - - +
25B ARG* 4.5 3.5 - - - -
26B GLU* 2.7 52.2 + - + +
28B ARG* 3.0 45.3 - - + +
46B GLU* 3.9 15.0 - - + +
47B GLU* 1.4 83.5 - - - +
49B GLN* 1.3 89.5 + - - +
51B GLY* 3.8 14.6 - - - +
52B GLU* 3.7 33.2 - - - +
53B VAL 4.4 2.9 - - - +
54B VAL* 4.1 2.9 - - - -
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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