Contacts of the strand formed by residues 153 - 158 (chain A) in PDB entry 5XTD
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 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LYS 3.9 2.8 + - - -
112A TYR* 3.9 19.2 - - + -
113A LEU* 4.1 6.0 + - - +
146A GLY* 4.9 0.5 - - - -
151A ALA* 3.3 22.3 - - - +
152A ARG* 1.3 82.9 - - + +
154A ALA* 1.3 65.6 + - - +
155A TYR* 4.0 7.2 - - + -
193A PHE* 4.4 7.9 - - - -
194A ASP 3.2 19.3 - - - +
196A PHE* 3.6 22.0 - - + -
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Residues in contact with ALA 154 (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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113A LEU* 3.9 12.1 - - + -
115A VAL* 5.3 0.7 - - - -
142A CYS* 4.2 14.1 - - + +
153A ALA* 1.3 81.7 - - - +
155A TYR* 1.3 65.1 + - - +
156A ILE* 3.6 10.2 + - - +
193A PHE* 3.6 30.3 - - + -
194A ASP 3.1 4.8 + - - -
195A VAL* 3.5 14.5 - - + +
196A PHE 3.1 16.5 + - - -
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Residues in contact with TYR 155 (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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112A TYR* 3.2 56.9 - + + -
113A LEU 3.0 12.3 + - - +
114A VAL* 4.5 13.9 - - + -
115A VAL* 2.9 25.4 + - - +
153A ALA* 4.0 6.7 - - + -
154A ALA* 1.3 71.9 - - - +
156A ILE* 1.3 62.5 + - - +
157A TYR 4.4 0.2 - - - -
196A PHE* 3.3 40.8 - + + -
198A VAL* 4.1 12.6 - - + -
216A ILE* 4.7 19.7 - - + -
235A VAL* 5.2 7.0 - - + -
236A PHE* 5.3 3.1 - + - -
98K GLN* 4.2 7.6 + - - -
69O ASN 4.6 0.3 + - - -
70O TYR* 4.1 18.4 - + - -
71O PRO* 4.0 22.0 - - - +
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Residues in contact with ILE 156 (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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115A VAL* 3.5 26.5 - - + -
117A ALA* 4.5 7.4 - - + -
138A LEU* 5.3 7.6 - - + -
139A LEU* 5.0 9.2 - - + -
142A CYS* 3.7 25.8 - - + -
154A ALA 3.6 10.3 - - - +
155A TYR* 1.3 81.1 - - - +
157A TYR* 1.3 70.2 + - - +
158A ILE* 4.3 11.0 - - + +
169A LEU* 4.8 16.6 - - + -
173A ILE* 5.3 4.5 - - + -
195A VAL* 5.0 9.2 - - + -
196A PHE 3.0 9.8 + - - +
197A VAL* 3.6 7.2 - - + -
198A VAL* 2.6 37.6 + - - +
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Residues in contact with TYR 157 (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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114A VAL* 5.4 1.0 - - - +
115A VAL 3.4 10.8 + - - +
117A ALA* 3.0 25.4 - - - +
118A ASP* 3.9 33.1 + - + -
155A TYR 4.4 0.2 - - - -
156A ILE* 1.3 71.4 - - - +
158A ILE* 1.3 92.2 + - - +
159A ARG* 3.7 10.8 - - + +
160A GLY 4.6 0.2 + - - -
198A VAL* 3.1 17.3 - - + -
199A ARG 3.7 5.4 - - - -
200A GLY* 3.2 40.6 - - - -
201A ALA* 3.9 2.1 + - - -
202A GLY 5.2 0.5 + - - -
203A ALA* 4.4 14.9 + - - +
206A CYS* 4.8 8.5 - - + -
212A LEU* 3.5 47.9 - - + +
215A SER* 4.6 11.9 - - - -
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Residues in contact with ILE 158 (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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117A ALA* 4.6 8.7 - - + +
131A LEU* 5.3 8.1 - - + -
156A ILE* 4.3 6.7 - - + +
157A TYR* 1.3 99.2 - - - +
159A ARG* 1.3 62.7 + - - +
162A PHE* 3.0 38.6 - - + +
165A GLU* 6.0 2.2 - - + -
166A ALA* 3.6 18.4 - - + +
169A LEU* 4.3 23.3 - - + -
197A VAL* 3.9 20.0 - - + -
198A VAL 2.5 22.8 + - - +
199A ARG* 3.2 8.9 - - + -
200A GLY 2.9 25.8 + - - -
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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