Contacts of the strand formed by residues 128 - 137 (chain A) in PDB entry 1I4W
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 ILE 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A THR* 4.7 11.8 - - - +
42A TYR* 4.3 3.1 - - - +
127A HIS* 1.3 82.3 - - - +
129A ASN* 1.3 78.0 + - - +
130A ASP* 3.1 6.8 + - - +
165A LYS* 3.0 38.4 - - + +
167A LYS* 4.1 27.1 - - + +
248A ASP* 3.6 32.1 - - + +
249A PRO 4.4 6.1 - - - +
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Residues in contact with ASN 129 (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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42A TYR* 3.5 11.8 - - - -
121A GLU 3.0 15.1 + - - +
123A GLN* 3.4 26.3 - - + +
127A HIS 3.2 4.9 + - - -
128A ILE* 1.3 84.8 - - - +
130A ASP* 1.3 63.4 + - - +
131A LYS* 2.9 17.8 - - - +
132A PHE* 3.1 24.4 - - - +
163A PHE* 2.9 27.0 - - - +
165A LYS 2.8 17.0 + - - +
166A VAL* 3.9 16.2 - - + +
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Residues in contact with ASP 130 (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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41A THR* 3.6 21.5 - - - +
42A TYR* 3.7 24.0 - - - +
43A LYS 5.4 0.8 + - - +
44A HIS* 5.5 5.2 + - - +
48A LEU* 4.6 2.3 - - - +
123A GLN* 2.8 32.3 + - - +
127A HIS* 4.7 10.8 + - + +
128A ILE* 3.1 7.1 + - - +
129A ASN* 1.3 73.8 - - - +
131A LYS* 1.3 74.5 + - - +
132A PHE 3.7 0.9 - - - -
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Residues in contact with LYS 131 (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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44A HIS* 6.3 1.1 - - - -
47A GLU* 3.7 42.8 - - + +
48A LEU* 3.4 14.1 - - - +
49A LYS* 2.9 30.5 + - - +
120A PRO* 5.8 0.3 - - - +
121A GLU* 3.1 47.6 + - + +
123A GLN* 3.6 7.3 - - - +
129A ASN* 2.9 2.8 - - - +
130A ASP* 1.3 102.3 + - - +
132A PHE* 1.3 61.1 + - - +
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Residues in contact with PHE 132 (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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42A TYR* 3.7 13.2 + - - -
48A LEU* 3.7 1.5 - - - +
49A LYS* 3.6 8.7 - - + -
51A LEU* 4.0 3.4 - - + -
118A PHE* 3.5 27.4 - + - -
120A PRO* 3.6 37.2 - - + -
121A GLU 4.9 1.3 - - - +
129A ASN* 3.1 22.6 - - - +
131A LYS* 1.3 82.8 - - - +
133A LEU* 1.3 73.6 + - - +
134A THR* 3.3 24.9 - - - -
160A LEU* 3.9 38.4 - - + -
163A PHE* 4.2 7.6 - + + -
166A VAL* 3.6 35.1 - - + +
167A LYS 4.5 0.3 + - - -
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Residues in contact with LEU 133 (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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38A LEU* 4.4 11.4 - - + -
42A TYR* 3.3 29.6 - - + +
48A LEU* 4.1 15.3 - - + -
49A LYS 3.2 6.8 + - - +
50A VAL* 3.2 15.9 - - + +
51A LEU 3.0 22.9 + - - -
64A PHE* 3.9 33.4 - - + -
132A PHE* 1.3 77.1 - - - +
134A THR* 1.3 71.0 + - - +
135A VAL* 4.7 3.6 - - + -
166A VAL* 5.7 0.2 - - - -
167A LYS* 3.6 16.6 - - + +
169A LEU* 3.5 30.1 - - + -
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Residues in contact with THR 134 (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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51A LEU* 3.3 18.3 - - + +
53A LEU* 4.2 15.7 - - + -
132A PHE* 3.3 30.3 - - - -
133A LEU* 1.3 75.1 + - - +
135A VAL* 1.3 73.9 + - - +
150A TRP* 4.9 1.8 - - + -
160A LEU* 4.2 12.6 - - + +
166A VAL* 5.3 0.5 - - - +
167A LYS 3.5 5.7 + - - -
168A MET* 3.2 54.9 - - - +
169A LEU* 3.2 4.9 + - - +
170A LEU* 5.2 0.2 - - - +
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Residues in contact with VAL 135 (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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50A VAL* 4.5 15.5 - - + -
51A LEU 2.8 10.1 + - - +
52A ASP* 3.4 15.9 - - - +
53A LEU* 2.8 27.1 + - - +
60A GLN* 2.9 32.5 - - - +
64A PHE* 6.0 4.9 - - + -
73A TYR* 4.7 5.6 - - + +
133A LEU* 4.7 6.3 - - + -
134A THR* 1.3 77.4 - - - +
136A ALA* 1.3 70.0 + - - +
169A LEU* 3.5 29.6 - - + +
170A LEU* 5.7 0.2 - - - -
171A TRP* 5.4 3.8 - - + -
244A LEU* 6.4 0.2 - - + -
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Residues in contact with ALA 136 (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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52A ASP* 5.4 0.2 - - - -
53A LEU* 3.4 21.5 - - + -
103A TYR* 3.9 5.4 - - - +
134A THR* 5.1 0.4 - - + -
135A VAL* 1.3 81.7 - - - +
137A ASN* 1.3 60.7 + - - +
138A VAL* 4.0 1.3 + - + -
150A TRP* 3.5 33.0 - - + -
169A LEU 3.1 9.0 + - - +
170A LEU* 3.3 11.8 - - + +
171A TRP* 3.0 26.6 + - - +
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Residues in contact with ASN 137 (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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20A PHE* 3.0 19.1 - - - -
21A LYS 3.2 20.4 + - - -
22A TYR* 3.3 23.3 - - + +
53A LEU 3.1 7.1 + - - -
54A TYR* 3.5 24.6 - - + +
103A TYR* 2.9 15.1 + - - -
136A ALA* 1.3 70.3 - - - +
138A VAL* 1.3 62.6 + - - +
139A THR* 2.5 41.5 + - - +
171A TRP* 3.9 23.9 - - + +
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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