Contacts of the strand formed by residues 130 - 140 (chain B) in PDB entry 4XXD
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 THR 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 4.6 19.6 - - + -
129B GLY* 1.3 79.9 + - - +
131B ALA* 1.3 62.4 + - - +
132B ALA 4.5 0.2 + - - -
178B THR* 4.2 29.2 - - + -
179B VAL 3.9 5.2 - - - +
180B PRO* 4.6 1.3 - - - -
181B SER* 3.9 3.4 + - - -
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 5.0 0.9 - - - -
121B PRO* 5.1 6.1 - - + -
122B SER 5.6 5.2 - - - +
130B THR* 1.3 77.1 - - - +
132B ALA* 1.3 61.4 + - - +
133B LEU* 5.7 0.7 - - + -
177B VAL 3.8 0.7 - - - +
178B THR* 3.4 4.1 - - - -
179B VAL* 2.7 47.6 + - + +
180B PRO 4.4 0.4 - - - -
181B SER* 3.8 15.5 - - - +
184B LEU* 4.0 25.6 - - + -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A PHE* 3.6 48.7 - - + -
118A PHE* 3.2 23.8 - - + -
135A LEU* 4.0 11.0 - - + -
121B PRO* 3.7 13.6 - - - +
122B SER 4.8 1.2 + - - -
131B ALA* 1.3 72.7 - - - +
133B LEU* 1.3 61.3 + - - +
176B VAL* 6.2 0.2 - - + -
177B VAL 3.8 4.3 - - - +
178B THR* 4.6 7.2 - - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 4.0 7.2 - - - -
119B LEU 3.4 13.5 - - - +
121B PRO* 3.9 28.5 - - + -
131B ALA 5.3 0.7 - - - +
132B ALA* 1.3 75.5 - - - +
134B GLY* 1.3 56.2 + - - +
149B TRP* 3.8 28.3 - - + -
176B VAL* 3.4 5.1 - - - +
177B VAL* 2.8 47.8 + - + +
179B VAL* 3.8 26.9 - - + -
184B LEU* 4.2 3.6 - - + -
189B TYR* 3.9 27.8 - - + -
206B VAL* 4.1 11.2 - - + +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 2.8 40.7 + - - +
133B LEU* 1.3 77.9 - - - +
135B CYS* 1.3 68.7 + - - -
149B TRP* 3.6 12.1 - - - -
175B SER 3.2 13.2 - - - -
176B VAL* 4.0 1.1 - - - -
206B VAL* 3.4 8.1 - - - +
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 4.4 8.3 - - + -
117B PHE 3.3 7.9 - - - +
118B PRO* 4.3 5.4 - - - -
119B LEU* 3.5 8.2 - - - +
134B GLY* 1.3 82.4 - - - -
136B LEU* 1.3 61.1 + - - +
137B VAL* 4.0 5.5 + - + +
147B VAL* 5.7 0.2 - - + -
149B TRP* 3.6 5.4 - - + -
174B SER* 3.4 3.3 - - - -
175B SER* 2.9 34.7 + - - +
191B CYS* 2.8 39.3 - - - -
204B LYS* 4.4 5.8 - - - -
206B VAL* 3.1 23.3 - - - -
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 4.3 2.5 - - - +
131A SER* 3.7 32.1 - - - +
133A VAL* 4.7 15.5 - - + -
178A THR* 4.8 10.3 - - + +
115B SER 3.3 5.2 - - - +
116B VAL* 3.5 2.4 - - - +
117B PHE* 2.7 64.0 + - + +
119B LEU* 4.0 15.4 - - + +
135B CYS* 1.3 71.8 - - - +
137B VAL* 1.3 59.2 + - - +
138B LYS* 4.2 13.0 - - + -
172B SER* 3.7 22.4 - - - +
173B LEU 3.7 15.3 - - - +
174B SER* 4.4 4.7 - - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PRO* 3.8 23.3 - - + -
115B SER 3.7 3.6 - - - -
116B VAL* 4.6 5.2 - - + +
135B CYS* 4.6 8.1 - - + +
136B LEU* 1.3 74.1 - - - +
138B LYS* 1.3 57.5 + - - +
140B TYR* 3.6 14.7 - - + -
145B VAL* 4.0 9.2 - - + -
147B VAL* 3.9 14.8 - - + -
172B SER* 3.2 4.0 - - - -
173B LEU* 2.8 51.7 + - + +
175B SER 5.7 0.7 - - - +
193B VAL* 3.8 40.4 - - + -
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLN* 3.9 17.9 - - - +
129A THR* 4.2 15.4 - - - +
131A SER* 3.3 22.0 - - - +
178A THR* 6.1 1.1 - - - -
180A THR* 4.4 14.7 - - - +
114B PRO* 3.3 2.9 - - - +
115B SER* 2.8 42.2 + - - +
117B PHE* 4.7 11.0 - - + -
136B LEU* 4.2 16.6 - - + -
137B VAL* 1.3 74.1 - - - +
139B ASP* 1.3 89.3 + - - +
140B TYR 3.7 1.6 - - - -
166B GLN* 3.3 19.5 + - - +
171B TYR 3.7 0.7 - - - -
172B SER* 3.4 17.9 - - - +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS* 2.7 41.8 + - - +
113B GLY 3.3 7.4 - - - +
115B SER* 5.0 6.1 + - - +
138B LYS* 1.3 98.8 + - - +
140B TYR* 1.3 56.9 + - - +
166B GLN* 2.8 31.2 + - - +
168B SER* 4.3 4.2 + - - -
170B LEU* 3.9 25.2 - - + +
171B TYR 3.0 12.0 + - - -
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Residues in contact with TYR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LYS 3.3 14.6 - - - +
114B PRO* 3.6 34.5 - - + -
137B VAL* 3.6 27.1 - - + -
139B ASP* 1.3 73.3 - - - +
141B PHE* 1.3 60.5 + - - +
142B PRO 3.6 20.0 - - - -
143B GLU* 4.4 8.7 + - + -
145B VAL* 3.6 25.7 + - + +
163B ALA* 3.3 13.7 - - - +
170B LEU* 3.6 3.9 - - - -
171B TYR* 2.7 80.4 + - + +
172B SER* 3.9 1.6 - - - -
173B LEU* 3.2 27.8 - - + +
195B HIS* 3.7 7.4 - - - +
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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