Contacts of the strand formed by residues 26 - 35 (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 GLU 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.0 9.2 - - + +
19B VAL 3.2 13.0 - - - +
20B ARG* 3.9 26.7 + - + -
24B GLY 3.5 5.6 + - - +
25B ARG* 1.3 76.5 - - - +
27B PHE* 1.3 63.8 + - - +
28B ARG* 6.0 0.3 - - - -
47B GLU* 3.5 5.5 - - - +
48B ILE* 2.7 61.1 + - + +
49B GLN* 6.4 0.2 - - - -
25C ARG* 5.9 0.7 + - - -
55C ARG* 3.1 39.7 + - - -
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Residues in contact with PHE 27 (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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69A PHE* 3.6 35.0 - + - -
17B VAL 3.7 0.3 - - - +
18B ILE* 3.2 7.1 - - - +
19B VAL* 2.8 42.1 + - + +
21B LEU* 4.0 30.5 - - + -
25B ARG* 4.8 2.2 - - + -
26B GLU* 1.3 79.9 - - - +
28B ARG* 1.3 63.7 + - - +
29B GLY 4.3 0.4 - - - -
42B LEU* 3.8 17.3 - - + -
45B ALA* 4.1 15.3 - - + -
46B GLU 3.4 12.6 - - - -
47B GLU* 4.3 26.7 - - + -
57B VAL* 4.5 8.7 - - + -
60B VAL* 4.1 27.6 - - + -
62B ILE* 4.6 7.4 - - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 6.1 1.8 - - - +
17B VAL 3.4 4.4 + - - +
18B ILE* 3.4 43.2 - - + +
26B GLU* 6.0 0.2 - - - -
27B PHE* 1.3 78.8 - - - +
29B GLY* 1.3 58.7 + - - +
44B ASP 3.7 1.4 - - - +
45B ALA* 3.0 22.1 - - - -
46B GLU* 3.1 29.2 + - - +
48B ILE* 3.0 34.6 - - + +
51B GLY 5.3 3.6 - - - -
73B ALA 4.1 8.6 + - - -
74B PRO 4.5 9.1 + - - -
75B GLY* 3.8 25.1 + - - -
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Residues in contact with GLY 29 (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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16B PRO* 4.3 5.6 - - - +
17B VAL* 3.0 35.3 + - - +
27B PHE 4.3 0.2 - - - -
28B ARG* 1.3 75.4 - - - +
30B THR* 1.3 63.7 + - - -
42B LEU* 4.5 7.9 - - - +
43B LEU 3.6 2.9 - - - -
44B ASP 3.4 14.8 - - - -
45B ALA* 4.1 4.9 - - - +
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Residues in contact with THR 30 (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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14B LYS* 3.2 42.0 - - - +
15B SER 3.9 4.9 - - - +
16B PRO* 4.3 5.5 - - + +
29B GLY* 1.3 70.6 - - - -
31B LEU* 1.3 65.7 + - - +
32B ASP* 3.2 2.2 + - - -
42B LEU* 3.3 3.5 - - - -
43B LEU* 2.9 53.2 + - + +
44B ASP* 4.2 4.7 + - - +
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Residues in contact with LEU 31 (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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9B LEU* 3.6 42.4 - - + +
12B SER* 4.0 16.8 - - - +
13B LEU* 4.5 9.6 - - + +
14B LYS* 2.8 29.6 + - - -
15B SER 3.2 15.8 + - - +
17B VAL* 4.0 16.6 - - + -
29B GLY 3.5 3.4 + - - -
30B THR* 1.3 71.4 - - - +
32B ASP* 1.3 59.0 + - - +
33B GLY 3.3 26.5 - - - +
34B TYR* 5.0 1.8 - - + -
40B LEU* 4.5 16.8 - - + -
41B VAL 3.8 6.5 - - - +
42B LEU* 3.9 13.2 - - + -
70B VAL* 5.3 3.6 - - + -
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Residues in contact with ASP 32 (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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3A PRO* 4.0 23.2 - - - +
4A ARG 5.4 0.2 + - - -
8A VAL* 4.6 7.4 - - - +
11A ARG* 4.8 8.2 + - - -
13B LEU* 3.1 17.3 - - - +
14B LYS* 5.1 4.6 + - - +
30B THR* 3.2 1.0 + - - -
31B LEU* 1.3 73.5 - - - +
33B GLY* 1.3 58.2 + - - +
41B VAL* 2.7 39.4 + - + +
43B LEU* 3.5 33.6 - - + +
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Residues in contact with GLY 33 (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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3A PRO* 4.3 18.4 - - - -
13B LEU* 3.9 7.2 - - - -
31B LEU* 3.3 17.4 - - - +
32B ASP* 1.3 80.7 - - - +
34B TYR* 1.3 69.9 + - - +
40B LEU* 3.9 0.2 - - - -
41B VAL* 3.4 24.1 + - - +
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Residues in contact with TYR 34 (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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3A PRO 4.4 2.4 + - - +
4A ARG* 4.0 12.8 + - - -
5A PRO* 3.6 15.4 - - - +
6B LEU* 3.3 31.3 + - + +
9B LEU* 4.0 23.3 - - + -
10B ASN* 3.0 48.4 + - - +
13B LEU* 3.9 21.3 - - + -
31B LEU* 5.0 3.4 - - + -
33B GLY* 1.3 79.9 - - - +
35B ASP* 1.3 72.7 + - - +
36B ILE 5.6 0.2 - - - -
38B MET* 5.4 0.9 - - - -
39B ASN 3.2 18.2 - - - +
40B LEU* 4.0 13.2 - - + -
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Residues in contact with ASP 35 (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* 4.7 9.4 - - - +
5A PRO* 3.2 31.8 - - + +
6A LEU* 4.8 5.9 + - - +
6B LEU* 5.4 1.3 - - - -
34B TYR* 1.3 87.6 - - - +
36B ILE* 1.3 63.9 + - + +
37B HIS* 2.4 16.2 + - - +
38B MET* 2.4 37.1 + - - -
39B ASN* 3.1 32.4 + - - -
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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