Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 1XTD
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 VAL 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER* 3.5 5.0 - - - -
102A VAL* 3.0 46.2 + - + +
142A ILE* 4.0 22.0 - - + -
145A GLN* 3.5 17.5 - - + -
146A PHE* 3.3 43.6 - - + +
150A LYS 3.5 3.5 + - - +
151A GLU* 1.3 76.2 - - - +
153A LEU* 1.3 62.3 + - - +
154A VAL* 4.3 2.7 - - + -
168A THR* 3.5 22.0 - - - +
169A LYS 4.2 1.6 - - - +
170A ASN* 3.7 6.7 - - - +
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Residues in contact with LEU 153 (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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99A THR* 4.2 14.8 - - + -
100A TYR 3.2 18.4 - - - +
101A SER* 3.8 20.2 - - - -
151A GLU* 3.8 10.3 + - - +
152A VAL* 1.3 72.3 - - - +
154A VAL* 1.3 63.7 + - - +
155A VAL 4.2 0.3 + - - -
168A THR* 3.5 4.0 + - - -
169A LYS* 2.7 64.0 + - + +
170A ASN 4.3 4.7 - - - +
171A ALA* 4.3 28.7 - - + +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 3.5 3.5 - - - +
100A TYR* 2.9 44.6 + - + +
102A VAL* 3.7 19.1 - - + -
117A LEU* 5.2 1.8 - - + -
119A LEU* 3.9 31.6 - - + -
142A ILE* 3.9 31.9 - - + -
152A VAL* 4.0 3.8 + - + -
153A LEU* 1.3 76.0 - - - +
155A VAL* 1.3 61.4 + - - +
156A VAL* 3.9 3.2 + - + -
165A VAL* 3.8 22.9 - - + -
167A GLN 3.7 3.4 - - - +
168A THR* 4.4 1.8 - - - +
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Residues in contact with VAL 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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97A THR* 3.4 33.4 - - + -
98A PHE 3.7 4.3 - - - +
99A THR* 4.2 7.6 - - - +
153A LEU 5.0 0.2 - - - +
154A VAL* 1.3 73.2 - - - +
156A VAL* 1.3 60.0 + - - +
157A VAL* 3.9 10.7 + - + -
165A VAL* 3.4 3.6 - - - -
166A LEU 3.0 26.0 + - - -
167A GLN* 3.2 46.1 + - + +
169A LYS* 3.8 24.9 - - + +
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Residues in contact with VAL 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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96A LYS 3.9 0.3 - - - +
97A THR* 3.4 4.3 - - - +
98A PHE* 2.8 46.6 + - + +
100A TYR* 3.7 29.4 - - + -
119A LEU* 4.5 3.4 - - + -
130A LEU* 4.0 21.1 - - + -
154A VAL* 4.6 2.5 - - + -
155A VAL* 1.3 74.8 - - - +
157A VAL* 1.3 68.0 + - - +
158A SER* 4.1 1.6 + - - -
163A GLU* 3.8 26.5 - - + +
164A GLN 3.4 11.0 - - - +
165A VAL* 3.9 22.0 - - + -
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Residues in contact with VAL 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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41A TYR* 5.5 1.6 - - - +
74A ILE* 4.3 11.7 - - + -
75A PHE* 3.5 6.2 - - + -
95A VAL* 3.4 30.7 - - + -
96A LYS 3.4 4.7 - - - +
97A THR* 4.4 7.6 - - + +
155A VAL* 4.2 15.9 - - + -
156A VAL* 1.3 77.1 - - - +
158A SER* 1.3 64.1 + - - +
163A GLU* 3.6 1.4 - - - -
164A GLN 2.9 30.4 + - - +
166A LEU* 3.5 41.7 - - + -
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Residues in contact with SER 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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75A PHE* 4.1 1.6 - - - -
94A PHE 3.9 0.6 - - - +
95A VAL* 3.5 5.2 - - - +
96A LYS* 3.1 43.5 + - - +
98A PHE* 5.5 5.6 - - - -
156A VAL* 4.1 1.5 + - - -
157A VAL* 1.3 74.7 - - - +
159A ALA* 1.3 68.0 + - - +
161A GLY* 5.3 3.8 + - - -
162A THR 3.5 6.6 + - - -
163A GLU* 3.7 24.2 - - - +
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Residues in contact with ALA 159 (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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48A PRO* 4.1 17.9 - - + -
74A ILE* 4.3 2.7 - - + -
75A PHE* 3.5 22.9 - - + -
93A PRO* 4.6 3.1 - - + -
94A PHE 3.8 16.8 - - - +
95A VAL* 4.3 12.3 - - + -
158A SER* 1.3 79.2 + - - +
160A MSE 1.3 72.9 + - + +
161A GLY 3.2 2.7 + - - -
162A THR* 3.1 17.6 + - - +
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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