Contacts of the strand formed by residues 141 - 146 (chain A) in PDB entry 1XNB
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TYR 3.7 4.5 - - - -
54A ASN* 3.0 17.6 - - - +
140A SER* 1.3 75.4 - - - +
142A ALA* 1.3 59.8 + - - +
143A THR* 5.0 1.7 + - - -
185A TRP* 3.5 30.1 - - + -
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Residues in contact with ALA 142 (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 ILE 3.9 0.2 - - - +
52A ASN* 3.3 6.4 - - - +
53A TYR* 2.8 62.4 + - + +
136A ARG* 3.5 28.9 - - + +
137A PRO 5.8 2.0 - - - +
140A SER* 3.3 6.0 + - - +
141A ASN* 1.3 73.2 - - - +
143A THR* 1.3 64.6 + - - +
185A TRP* 5.4 0.3 - - - -
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Residues in contact with THR 143 (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 THR* 3.4 29.8 - - + -
51A ILE 3.4 4.7 - - - +
52A ASN* 3.5 14.3 + - - +
101A ASP* 3.1 30.7 - - - +
136A ARG* 2.9 24.9 + - - +
141A ASN 5.0 1.6 + - - -
142A ALA* 1.3 78.3 - - - +
144A ILE* 1.3 66.8 + - - +
145A THR* 4.0 2.2 - - - +
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Residues in contact with ILE 144 (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 THR* 3.6 0.9 - - - -
51A ILE* 2.8 41.2 + - + +
53A TYR* 3.9 7.6 - - + -
68A LEU* 4.2 26.5 - - + -
81A VAL* 4.1 27.1 - - + +
83A ASP* 3.7 29.6 - - + +
101A ASP* 3.5 3.1 - - - -
105A TYR* 4.9 2.0 - - - +
136A ARG* 4.1 1.8 - - - +
143A THR* 1.3 80.1 - - - +
145A THR* 1.3 59.0 + - - +
146A PHE* 3.2 13.0 + - + +
149A HIS* 4.3 10.5 - - + +
169A MET* 3.6 30.5 - - + -
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Residues in contact with THR 145 (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 THR* 4.2 18.3 - - + +
100A SER* 3.8 0.5 + - - -
101A ASP* 2.7 33.3 + - - -
143A THR* 4.0 8.0 - - - +
144A ILE* 1.3 68.7 - - - +
146A PHE* 1.3 65.4 + - - +
147A THR* 3.6 23.6 - - + -
148A ASN* 3.1 35.2 + - - +
149A HIS* 3.6 6.8 - - - -
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Residues in contact with PHE 146 (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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46A SER 3.4 13.9 - - - -
47A PRO* 4.0 1.8 - - + +
49A ARG 3.3 18.5 + - - +
51A ILE* 3.9 11.4 - - + -
68A LEU* 3.6 23.6 - - + -
79A TYR* 3.5 26.9 - + - -
81A VAL* 4.1 5.6 - - + -
144A ILE* 3.2 5.7 + - - -
145A THR* 1.3 72.9 - - - +
147A THR* 1.3 63.1 + - - +
149A HIS* 3.0 23.9 + - + -
150A VAL* 3.0 37.7 + - + +
153A TRP* 4.0 25.6 - + - -
160A LEU* 4.5 2.0 - - + -
164A TRP* 4.0 12.8 - + - -
167A GLN* 3.4 26.2 - - - -
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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