Contacts of the strand formed by residues 146 - 152 (chain A) in PDB entry 1XB2
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 GLY 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ASN 3.4 2.7 + - - +
60A VAL* 3.2 10.4 - - - -
61A GLY 3.1 21.7 + - - -
144A LEU* 3.4 4.0 - - - +
145A ASP* 1.3 83.1 - - - +
147A CYS* 1.3 66.2 + - - +
173A VAL* 3.8 7.2 - - - +
175A HIS 3.4 12.6 - - - -
247A ILE* 3.9 14.3 - - - +
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Residues in contact with CYS 147 (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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61A GLY 3.2 11.0 - - - +
63A ILE* 3.8 30.3 - - + -
144A LEU* 4.3 12.1 - - - -
146A GLY* 1.3 80.4 - - - -
148A ILE* 1.3 65.1 + - - +
149A LEU 3.9 0.7 - - - -
167A LEU* 5.8 1.1 - - - -
168A ALA* 4.1 15.0 - - - -
171A ILE* 5.3 1.3 - - - -
173A VAL* 3.8 26.9 - - + +
175A HIS 3.2 7.3 + - - +
176A VAL* 3.4 10.1 - - + +
177A VAL* 2.9 25.5 + - - +
247A ILE* 4.5 3.1 - - - +
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Residues in contact with ILE 148 (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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60A VAL* 4.7 14.4 - - + -
61A GLY 2.8 12.0 + - - +
62A THR* 3.3 9.8 - - + +
63A ILE* 3.0 23.3 + - - +
73A LEU* 4.3 13.2 - - + -
77A ILE* 5.4 3.6 - - + -
115A TYR* 4.8 3.4 - - - +
124A HIS* 3.9 26.9 - - + +
147A CYS* 1.3 76.1 - - - +
149A LEU* 1.3 59.6 + - - +
150A VAL* 3.9 18.6 - - + -
177A VAL* 3.2 12.8 - - + +
179A TYR* 4.8 2.2 - - + -
239A LEU* 4.6 18.8 - - + -
240A LEU* 6.6 0.2 - - + -
243A VAL* 3.9 29.6 - - + -
247A ILE* 6.2 0.7 - - + -
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Residues in contact with LEU 149 (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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63A ILE* 3.5 39.5 - - + +
64A GLY* 4.4 7.0 - - - -
147A CYS 3.9 2.2 - - - -
148A ILE* 1.3 70.1 - - - +
150A VAL* 1.3 60.3 + - - +
151A VAL* 3.8 23.3 - - + -
161A THR* 4.6 15.3 - - + +
164A HIS* 4.7 11.4 - - + +
165A LEU* 4.3 21.8 - - + -
176A VAL* 4.1 11.6 - - + +
177A VAL 2.9 9.0 + - - +
178A VAL* 3.4 19.8 - - + +
179A TYR 2.9 26.0 + - - -
199A ILE* 4.8 10.8 - - + -
203A LEU* 4.9 3.1 - - + -
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Residues in contact with VAL 150 (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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62A THR* 3.5 28.0 - - + -
63A ILE 3.0 6.1 + - - -
64A GLY* 3.8 17.0 - - - -
65A HIS 4.4 0.3 + - - -
68A HIS* 3.7 32.0 + - - +
69A GLY* 4.1 3.1 - - - +
70A LYS* 3.9 25.8 - - + +
73A LEU* 3.9 22.7 - - + -
148A ILE* 3.9 6.3 - - + -
149A LEU* 1.3 74.7 - - - +
151A VAL* 1.3 66.4 + - - +
179A TYR* 3.4 19.7 - - + +
181A ASN* 4.5 2.2 - - + -
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Residues in contact with VAL 151 (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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68A HIS* 3.9 6.7 - - + +
149A LEU* 3.8 28.5 - - + +
150A VAL* 1.3 79.0 - - - +
152A ALA* 1.3 61.7 + - - +
156A GLY* 3.5 33.9 - - - +
157A PRO* 3.7 9.0 - - + -
161A THR* 5.2 5.4 - - + +
178A VAL* 4.8 0.7 - - + -
179A TYR 3.0 7.7 + - - +
180A VAL* 3.2 7.0 - - - +
181A ASN* 2.8 32.4 + - - -
195A VAL* 4.6 2.5 - - + -
199A ILE* 3.9 31.9 - - + -
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Residues in contact with ALA 152 (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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67A ASP 5.3 0.9 - - - +
68A HIS* 3.2 46.3 + - + +
151A VAL* 1.3 74.7 - - - +
153A ALA* 1.3 56.9 + - - +
154A ASN* 4.4 4.7 - - + +
155A ASP* 4.1 11.7 - - - +
156A GLY* 2.7 35.3 + - - -
180A VAL* 4.7 0.2 - - - -
181A ASN* 3.1 11.0 - - + +
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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