Contacts of the strand formed by residues 156 - 166 (chain A) in PDB entry 2X1L
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TRP* 3.7 29.0 - - + -
126A TYR 3.3 20.0 - - - +
127A SER* 3.8 13.5 - - - +
134A PHE* 4.2 7.0 - - + -
139A THR* 3.9 7.9 - - + -
147A ARG* 3.1 44.8 + - + +
148A ILE 3.8 8.3 - - - -
149A ALA* 3.9 19.5 - - + -
155A PRO* 1.3 76.0 - - - +
157A THR* 1.3 62.2 + - - +
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Residues in contact with THR 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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125A TRP* 3.5 3.5 - - - -
126A TYR* 2.9 32.3 + - - -
128A ILE* 3.6 25.5 - - + +
155A PRO 5.1 1.2 + - - -
156A VAL* 1.3 74.9 - - - +
158A TRP* 1.3 75.0 + - - +
159A THR* 3.3 8.5 + - - +
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Residues in contact with TRP 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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123A LYS* 4.2 21.8 - - + -
124A GLY* 3.5 34.5 - - - -
125A TRP* 3.5 56.0 - + + -
136A GLU* 4.8 6.3 - - + -
157A THR* 1.3 82.2 - - - +
159A THR* 1.3 61.7 + - - +
160A GLU* 2.9 36.9 + - + +
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Residues in contact with THR 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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122A TYR* 3.8 16.3 - - + +
123A LYS* 3.4 4.9 - - - -
124A GLY 2.9 39.0 + - - -
126A TYR* 3.7 14.9 - - - +
133A PHE* 6.1 0.7 - - + -
157A THR* 3.3 16.3 + - - +
158A TRP* 1.3 75.1 + - - +
160A GLU* 1.3 68.5 + - - +
161A GLU* 3.3 34.8 - - + +
210A ARG* 3.7 17.4 + - - +
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Residues in contact with GLU 160 (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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122A TYR 3.4 5.6 - - - +
123A LYS* 3.3 37.8 - - + -
158A TRP* 2.9 35.0 + - + +
159A THR* 1.3 75.9 - - - +
161A GLU* 1.3 66.9 + - - +
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Residues in contact with GLU 161 (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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121A ALA* 4.8 1.3 - - - -
122A TYR* 2.8 43.0 + - + +
159A THR* 3.3 15.7 - - + +
160A GLU* 1.3 78.6 - - - +
162A GLN* 1.3 57.0 + - - +
163A THR* 3.3 14.2 + - + +
210A ARG* 3.0 39.6 + - - -
211A THR* 3.2 31.0 + - - +
212A THR* 2.9 38.8 + - + +
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Residues in contact with GLN 162 (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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119A LEU* 4.3 20.9 - - + +
120A ASP* 3.3 13.0 + - - +
121A ALA* 3.2 38.0 - - - +
161A GLU* 1.3 69.9 - - - +
163A THR* 1.3 60.0 + - - +
211A THR* 3.8 10.8 + - + +
225A HIS* 3.2 21.5 - - - -
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Residues in contact with THR 163 (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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119A LEU* 3.6 6.5 - - - +
120A ASP 2.9 31.9 + - - +
122A TYR* 3.6 9.9 - - + +
161A GLU* 3.3 32.0 + - + +
162A GLN* 1.3 78.1 - - - +
164A TYR* 1.3 62.2 + - - +
165A PHE* 3.6 18.2 - - - -
207A SER* 3.0 20.1 + - - +
209A SER* 3.3 31.2 - - - +
210A ARG* 4.6 4.3 - - - -
211A THR 5.3 0.4 - - - +
225A HIS* 4.3 0.9 - - - -
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Residues in contact with TYR 164 (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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108A TRP* 4.0 18.8 - + + -
117A ILE* 3.8 24.5 - - + -
118A TYR* 3.3 17.5 - - - -
119A LEU* 3.7 29.1 - - + +
163A THR* 1.3 74.7 + - - +
165A PHE* 1.3 56.3 + - - +
207A SER* 3.5 5.0 - - - -
208A ILE* 2.8 31.4 + - + -
209A SER* 2.8 29.1 + - - +
219A VAL* 4.6 2.9 - - + -
222A HIS* 3.0 47.1 + + + -
225A HIS* 3.7 32.5 + + + -
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Residues in contact with PHE 165 (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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116A ASP 3.3 0.9 - - - +
117A ILE* 3.2 10.0 - - - +
118A TYR* 2.8 56.1 + + + +
120A ASP* 3.6 36.8 - - + -
121A ALA 4.2 3.6 - - - -
122A TYR* 3.6 38.6 - + + -
163A THR* 3.6 22.0 - - - -
164A TYR* 1.3 73.2 - - - +
166A PHE* 1.3 61.1 + - - +
205A ASP* 4.0 20.9 - - + -
206A LEU 3.2 18.4 - - - -
207A SER* 3.6 12.3 - - - -
208A ILE* 3.9 4.7 - - - -
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Residues in contact with PHE 166 (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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111A MET* 3.6 24.7 - - + -
116A ASP* 3.3 15.3 - - + -
117A ILE* 4.8 2.2 - - + -
165A PHE* 1.3 73.4 - - - +
167A ARG* 1.3 61.2 + - - +
168A LEU* 2.8 35.5 + - + -
171A TYR* 3.9 11.2 - + - -
205A ASP* 3.5 6.7 - - - +
206A LEU* 2.7 32.9 + - + +
208A ILE* 3.8 25.8 - - + +
276A ALA* 3.3 44.9 - - + -
277A PHE* 3.5 18.8 - + + -
280A SER* 3.6 26.5 - - - -
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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