Contacts of the strand formed by residues 126 - 132 (chain B) in PDB entry 4IWN
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 ALA 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B GLN 3.3 7.9 - - - +
61B TYR* 3.8 30.3 - - + -
123B ILE* 4.1 2.2 - - + -
124B GLU 3.8 0.7 - - - -
125B ASN* 1.3 75.4 - - - +
127B SER* 1.3 60.8 + - - +
128B MET 4.2 1.8 - - - +
129B VAL* 4.0 19.5 - - + -
153B GLY 3.4 14.6 + - - +
154B LEU* 3.4 7.4 - - + +
155B ASN* 2.8 30.4 + - - +
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 3.3 25.6 - - - +
54B VAL* 3.5 18.5 - - - +
55B GLN* 3.9 9.9 - - - -
58B THR* 2.9 27.8 + - - -
59B GLN 3.0 8.8 + - - -
60B VAL* 4.2 0.2 - - - +
125B ASN 3.9 1.8 + - - -
126B ALA* 1.3 73.0 - - - +
128B MET* 1.3 61.7 + - - +
154B LEU* 4.2 0.4 - - - -
155B ASN* 3.9 6.0 - - - +
158B GLY* 3.2 13.0 - - - -
159B ALA 3.0 19.6 + - - -
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Residues in contact with MET 128 (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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46B ILE* 3.7 38.4 - - + +
49B LEU* 3.9 26.0 - - + +
50B ALA* 3.8 24.9 - - - -
53B PHE* 4.6 5.8 - - + -
54B VAL* 4.5 7.2 - - + -
59B GLN 3.9 2.3 + - - +
60B VAL* 3.2 24.6 - - + +
61B TYR 3.0 23.2 + - - -
74B VAL* 4.4 6.5 - - + -
126B ALA* 3.3 2.0 - - - +
127B SER* 1.3 85.5 + - - +
129B VAL* 1.3 73.3 + - - +
130B VAL* 4.1 11.7 - - + -
154B LEU* 4.2 0.4 - - - -
159B ALA* 3.3 13.5 - - + +
161B VAL* 4.2 5.4 - - + -
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 3.6 10.3 - - + +
63B LEU* 3.5 31.2 - - + -
123B ILE* 4.2 12.6 - - + -
126B ALA* 4.0 12.1 - - + -
128B MET* 1.3 79.5 - - - +
130B VAL* 1.3 68.7 + - - +
150B ILE* 3.6 29.6 - - + -
154B LEU* 3.6 20.2 - - + -
159B ALA 2.9 7.1 + - - +
160B LEU* 3.2 14.3 - - + +
161B VAL* 2.9 25.1 + - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.8 33.2 - - + -
60B VAL* 4.8 2.5 - - + -
61B TYR 3.0 15.9 + - - +
62B ASP* 3.9 10.2 - - + +
63B LEU* 2.8 35.5 + - - +
70B ALA* 4.1 11.0 - - + -
74B VAL* 4.7 8.5 - - + -
128B MET* 4.1 25.4 - - + -
129B VAL* 1.3 79.5 - - - +
131B LEU* 1.3 62.1 + - - +
132B ASN* 3.8 17.3 - - + +
161B VAL* 3.7 11.0 - - + +
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Residues in contact with LEU 131 (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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63B LEU* 3.7 24.5 - - + -
130B VAL* 1.3 72.5 - - - +
132B ASN* 1.3 59.0 + - - +
133B PHE 3.3 3.8 + - - -
134B THR* 3.6 32.7 + - + -
135B LEU* 4.2 10.1 - - + +
146B LEU* 4.2 18.4 - - + -
147B LEU* 4.1 19.5 - - + -
150B ILE* 3.8 25.1 - - + -
160B LEU* 4.1 7.3 - - + +
161B VAL 2.8 14.7 + - - +
162B LEU* 4.0 17.1 - - + +
163B SER 3.0 25.5 + - - +
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Residues in contact with ASN 132 (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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39B TYR* 3.9 6.1 - - - -
42B ILE* 3.5 10.5 - - - +
43B ILE* 3.5 20.6 - - - +
46B ILE* 3.9 11.5 - - + +
62B ASP* 5.3 0.6 + - - +
63B LEU 4.5 1.0 + - - -
70B ALA* 4.7 1.6 - - + -
130B VAL* 3.7 17.8 + - + -
131B LEU* 1.3 72.0 - - - +
133B PHE* 1.3 83.4 + - - +
134B THR* 3.4 4.0 + - - +
163B SER* 2.8 31.2 + - - -
301B GEK 2.9 51.3 + - - +
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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