Contacts of the strand formed by residues 134 - 145 (chain A) in PDB entry 1W21
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A CYS* 3.1 4.0 - - - +
131A ASP* 2.8 39.8 + - - +
133A GLN* 1.3 80.0 - - - +
135A CYS* 1.3 66.0 + - - -
136A ARG* 5.8 0.7 - - - -
1216B GLY 5.7 3.6 - - - -
1217B ARG* 3.7 16.8 - - - +
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Residues in contact with CYS 135 (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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106A LEU* 5.4 4.9 - - - -
128A LEU* 4.9 4.3 - - + -
129A SER 3.6 4.9 - - - +
130A CYS* 2.0 45.8 - - - -
134A GLY* 1.3 75.7 - - - -
136A ARG* 1.3 69.3 + - - +
168A GLU* 5.0 1.7 - - - +
169A MET* 3.3 45.6 + - + +
416A PHE* 4.7 5.6 - - + -
418A ASP* 4.0 16.2 - - - -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.3 8.4 - - - +
129A SER 2.9 32.0 + - - +
131A ASP* 5.0 11.2 - - - -
135A CYS* 1.3 79.6 - - - +
137A MET* 1.3 65.7 + - - +
138A PHE* 3.5 19.3 - - + -
166A SER* 3.0 42.6 + - - -
167A TRP* 3.5 23.5 - - - +
168A GLU* 3.8 11.0 - - - +
169A MET* 4.2 1.3 - - - +
177A ASN 5.4 1.2 + - - -
179A ARG* 3.6 44.1 - - - +
181A GLU* 5.0 0.4 + - - -
196A ARG* 5.5 6.7 - - - +
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Residues in contact with MET 137 (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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107A SER* 3.5 32.3 - - - +
108A LYS 4.5 1.3 - - - +
109A ASP* 4.1 16.8 - - + +
127A TYR 3.5 5.6 - - - +
128A LEU* 3.9 18.8 - - + -
136A ARG* 1.3 74.5 - - - +
138A PHE* 1.3 60.4 + - - +
166A SER* 3.1 5.9 - - - -
167A TRP* 3.0 66.6 + - + +
169A MET* 3.9 9.9 - - + -
170A GLY 3.4 16.6 - - - +
171A GLN 3.9 4.5 - - - +
451A ILE* 4.0 34.8 - - + -
453A ALA* 5.4 0.2 - - + -
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Residues in contact with PHE 138 (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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126A PRO* 3.1 3.7 - - - +
127A TYR* 2.8 65.7 + + + +
129A SER* 3.7 24.2 - - - -
136A ARG* 3.5 33.7 - - + -
137A MET* 1.3 77.5 - - - +
139A ALA* 1.3 64.8 + - - +
164A LEU* 4.1 13.7 - - + -
165A ILE 3.2 6.1 - - - -
166A SER* 3.6 23.1 - - - -
167A TRP* 3.9 5.2 - - - -
181A GLU* 4.0 12.3 - - + -
189A SER* 3.6 17.9 - - - -
196A ARG* 3.8 26.2 - - - -
451A ILE* 4.5 0.7 - - - +
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Residues in contact with ALA 139 (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 THR* 3.9 17.3 - - + +
124A ARG 3.8 5.8 - - - +
125A GLU 3.7 11.0 - - - -
126A PRO* 3.7 15.3 - - + -
138A PHE* 1.3 79.2 - - - +
140A LEU* 1.3 61.0 + - - +
141A SER 3.7 0.4 - - - -
164A LEU* 3.4 10.8 - - - +
165A ILE* 2.9 34.7 + - - +
167A TRP* 3.8 19.4 - - + -
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Residues in contact with LEU 140 (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 THR* 3.2 3.1 - - - -
124A ARG 3.0 20.2 + - - +
125A GLU* 3.8 25.1 + - + +
139A ALA* 1.3 72.0 - - - +
141A SER* 1.3 61.3 - - - +
162A ARG* 2.8 38.5 + - - +
163A ALA 3.4 1.1 - - - +
164A LEU* 4.0 20.2 - - + +
184A GLY 3.8 19.7 - - - +
185A TRP* 3.3 28.7 - - - +
186A SER 3.8 4.3 - - - +
187A SER* 4.1 20.2 - - - +
200A CYS* 5.3 0.2 - - - -
234A GLU* 3.8 17.7 - - - +
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Residues in contact with SER 141 (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 LEU* 4.0 16.6 - - - +
122A VAL 3.5 9.7 + - - -
123A THR* 4.2 4.0 - - - -
139A ALA 3.6 3.0 + - - -
140A LEU* 1.3 78.1 - - - +
142A GLN* 1.3 61.6 + - - +
143A GLY* 3.0 16.9 + - - -
161A PHE 5.4 0.2 - - - -
162A ARG* 3.1 28.1 + - - -
163A ALA* 2.9 19.9 + - - -
165A ILE* 4.2 25.0 - - - +
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Residues in contact with GLN 142 (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 VAL* 2.8 39.0 + - + +
123A THR* 4.7 2.4 + - - -
124A ARG* 5.6 2.6 - - - +
141A SER* 1.3 73.3 - - - +
143A GLY* 1.3 59.0 + - - +
144A THR* 3.4 1.1 - - + -
154A THR* 3.1 36.8 + - + -
155A ILE 5.0 0.2 - - - -
156A HIS 3.0 26.2 + - - +
159A SER* 4.4 0.9 + - - -
161A PHE 3.4 8.3 - - - +
162A ARG* 3.3 38.8 - - - +
447A THR 5.4 0.4 + - - -
1479A GOL 2.8 32.9 + - - -
2113C ARG* 3.0 23.9 + - - -
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Residues in contact with GLY 143 (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 LEU* 5.1 0.2 - - - -
141A SER* 3.0 12.9 + - - -
142A GLN* 1.3 78.7 - - - +
144A THR* 1.3 57.0 + - - +
161A PHE 3.4 15.1 + - - -
2110C ASN* 4.3 9.4 - - - +
2113C ARG* 2.9 36.3 + - - +
2114C ILE* 3.8 18.0 - - - +
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Residues in contact with THR 144 (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 LEU* 3.4 9.2 - - - +
122A VAL* 2.7 56.2 + - + +
142A GLN 3.9 9.2 - - - +
143A GLY* 1.3 80.3 - - - +
145A THR* 1.3 62.7 + - - +
148A GLY* 4.6 2.8 + - - -
150A HIS* 3.2 44.8 + - - +
151A ALA* 3.3 6.0 + - - -
154A THR* 4.0 5.6 - - + -
2113C ARG* 3.9 5.5 + - - +
2114C ILE* 4.1 12.5 - - - +
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Residues in contact with THR 145 (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 HIS* 4.3 5.4 - - + -
120A ILE 3.2 23.3 - - - +
121A LEU* 4.8 1.1 - - + -
122A VAL* 3.6 5.6 - - - +
144A THR* 1.3 88.2 + - - +
146A LEU* 1.3 65.2 + - - +
147A ARG 4.3 0.9 - - - -
148A GLY* 3.2 13.9 + - - -
151A ALA* 3.7 3.1 - - - +
175A PRO* 4.2 16.4 - - + -
2113C ARG 5.4 0.4 + - - -
2114C ILE* 4.6 9.4 + - + +
2117C ASP* 3.0 30.8 + - - +
2118C ALA* 4.0 26.9 - - + -
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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