Contacts of the strand formed by residues 12 - 19 (chain B) in PDB entry 1I72
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 LYS 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 3.4 2.6 - - - -
81A THR 2.8 20.0 + - - +
82A CYS* 4.1 4.0 + - - +
83A GLY 3.4 16.4 + - - -
85A THR* 2.8 36.6 + - - +
87A LEU* 3.1 32.2 - - + +
112A TYR* 3.5 16.6 - - + +
113A SER 3.8 4.0 - - - -
114A ARG* 4.1 2.7 - - - -
117A PHE* 3.8 20.3 - - + -
123A GLN* 3.0 27.1 + - - +
127A HIS* 3.6 35.2 - - + +
10B THR 5.2 0.2 - - - +
11B GLU* 1.3 76.3 - - - +
13B LEU* 1.3 58.9 + - - +
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Residues in contact with LEU 13 (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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78A ILE* 4.0 17.5 - - + -
79A LEU 3.8 0.4 - - - +
80A LYS* 3.8 26.9 - - + -
111A PHE 3.5 1.4 - - - +
112A TYR* 3.2 9.1 - - - -
113A SER* 2.7 50.1 + - - +
178A GLU* 3.5 34.1 - - - +
256A GLU* 3.7 24.5 - - - +
350A PUT 3.4 28.7 + - - +
11B GLU 5.2 1.6 - - - +
12B LYS* 1.3 74.1 - - - +
14B LEU* 1.3 64.8 + - - +
15B GLU* 5.7 0.7 - - + -
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Residues in contact with LEU 14 (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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77A PHE* 3.8 9.6 - - + +
78A ILE* 3.4 5.4 - - - +
79A LEU* 2.9 41.3 + - + +
87A LEU* 3.6 29.4 - - + +
88A LEU* 5.2 3.1 - - + -
90A ALA* 5.7 1.1 - - + -
91A LEU* 4.4 19.1 - - + +
94A LEU* 4.3 24.0 - - + -
110A PHE* 3.5 37.5 - - + -
111A PHE 3.4 5.8 - - - +
112A TYR* 4.4 8.3 - - + -
12B LYS 4.2 0.2 - - - -
13B LEU* 1.3 75.4 - - - +
15B GLU* 1.3 63.2 + - - +
16B VAL* 3.9 8.1 - - + -
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Residues in contact with GLU 15 (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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76A ARG* 4.1 9.6 - - + -
77A PHE 3.2 9.2 - - - +
78A ILE* 3.7 25.9 - - + +
110A PHE* 3.6 1.2 - - - -
111A PHE* 2.8 38.0 + - + +
239A TYR* 4.2 6.8 + - - -
256A GLU* 4.7 1.2 - - - +
350A PUT 2.7 66.0 + - - +
13B LEU* 5.3 0.9 - - + +
14B LEU* 1.3 76.0 - - - +
16B VAL* 1.3 67.6 + - - +
17B TRP* 2.8 28.4 + - + +
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Residues in contact with VAL 16 (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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75A ARG 3.7 1.4 - - - +
76A ARG* 3.4 3.6 - - - +
77A PHE* 2.9 35.8 + - + +
91A LEU* 4.9 2.0 - - + -
94A LEU* 4.3 14.8 - - + -
95A LEU* 5.0 0.4 - - + -
107A ILE* 4.0 25.8 - - + -
109A SER 3.4 9.6 - - - +
110A PHE* 3.8 17.9 - - + -
14B LEU* 3.9 18.8 - - + -
15B GLU* 1.3 80.5 - - - +
17B TRP* 1.3 67.8 + - - +
18B PHE* 3.8 30.5 - - + -
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Residues in contact with TRP 17 (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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75A ARG* 3.4 55.0 - - + -
76A ARG* 3.5 41.3 - - + +
107A ILE* 3.7 5.2 - - - +
108A GLN* 2.8 42.3 + - + +
109A SER* 2.8 38.4 + - - +
111A PHE* 4.5 2.7 - + - -
172A GLN* 4.1 20.0 - - - -
174A ASP* 3.8 26.2 - - - -
318A TYR* 4.4 9.0 + - - -
350A PUT 4.9 0.2 - - - -
15B GLU* 2.8 30.1 + - + -
16B VAL* 1.3 76.9 - - - +
18B PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 18 (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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75A ARG* 2.8 43.7 + - - +
77A PHE* 4.2 15.5 - - + -
94A LEU* 4.0 15.3 - - + -
95A LEU* 3.7 29.6 - - + -
98A ALA* 3.6 25.6 - - + -
104A PHE* 3.5 30.9 - + + -
106A SER 3.6 14.8 - - - -
107A ILE* 4.5 2.7 - - + -
108A GLN* 4.5 4.3 - - - +
16B VAL* 3.8 31.0 - - + -
17B TRP* 1.3 76.6 - - - +
19B SER* 1.3 64.5 + - - +
32B LEU* 3.9 19.1 - - + -
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Residues in contact with SER 19 (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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104A PHE* 3.5 13.4 - - - -
105A ASP 3.3 5.9 + - - -
106A SER* 3.0 44.2 + - - +
107A ILE 4.5 0.5 - - - -
108A GLN* 4.3 21.6 + - - +
18B PHE* 1.3 78.7 - - - +
20B ARG* 1.3 64.9 + - - +
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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