Contacts of the strand formed by residues 125 - 141 (chain A) in PDB entry 2WV4
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A VAL 3.7 1.0 - - - +
120A ASN* 4.1 7.4 - - - -
121A ASN 2.7 23.8 + - - -
122A ALA* 4.6 1.2 - - - -
123A ASP 4.4 0.2 - - - +
124A VAL* 1.3 90.8 - - - +
126A ARG* 1.3 66.6 + - - -
127A LEU 3.2 3.5 + - - -
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Residues in contact with ARG 126 (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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13A MET* 6.4 2.5 - - + -
119A VAL 3.4 9.0 - - - +
120A ASN* 4.1 17.1 + - + +
124A VAL 4.2 1.4 - - - +
125A GLY* 1.3 70.7 - - - -
127A LEU* 1.3 58.7 + - - +
128A ILE* 6.2 1.3 - - + -
126B ARG 4.1 17.9 + - - +
127B LEU* 3.8 13.2 - - + -
128B ILE* 3.2 24.1 + - - +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A VAL* 2.7 44.3 + - + +
124A VAL* 4.0 29.8 - - + +
125A GLY 3.2 0.2 + - - -
126A ARG* 1.3 75.3 - - - +
128A ILE* 1.3 84.1 + - - +
129A PHE* 3.8 19.7 - - + -
162A TYR* 3.4 32.8 - - + +
128B ILE* 3.1 29.4 - - + +
130B SER* 4.7 9.6 - - - +
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Residues in contact with ILE 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 4.0 18.6 - - - +
13A MET* 4.5 13.0 - - + -
116A VAL* 3.5 29.8 - - + -
117A GLY 3.3 2.0 - - - +
118A VAL* 3.8 33.0 - - + -
119A VAL 4.4 0.9 - - - +
126A ARG* 6.2 0.9 - - + -
127A LEU* 1.3 89.3 - - - +
129A PHE* 1.3 62.1 + - - +
127B LEU* 4.1 23.3 - - + -
128B ILE 2.7 12.0 + - - +
129B PHE* 3.1 12.3 - - + +
130B SER 2.9 23.6 + - - +
157B ALA* 4.1 13.8 - - + +
162B TYR* 4.9 1.6 - - - +
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 5.8 2.5 - - + -
116A VAL* 3.4 4.9 - - - +
117A GLY* 2.6 62.7 + - - -
119A VAL* 3.5 24.7 - - + -
127A LEU* 3.8 10.1 - - + -
128A ILE* 1.3 76.5 - - - +
130A SER* 1.3 70.0 + - - +
154A TYR* 4.3 14.8 - + - -
156A ALA* 4.6 4.3 - - + -
157A ALA 4.7 5.2 - - - +
158A THR* 3.6 27.8 - - + -
162A TYR* 3.5 26.0 - + + -
165A GLY* 6.1 0.9 - - - -
167A VAL* 5.0 3.8 - - + -
181A HIS* 4.3 18.6 - + + -
130B SER* 3.3 22.0 - - - +
157B ALA* 4.8 1.1 - - - -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL 3.3 7.9 - - - -
129A PHE* 1.3 80.1 - - - +
131A GLY* 1.3 59.9 + - - +
156A ALA* 3.5 16.9 - - - +
157A ALA 4.9 1.4 + - - -
130B SER 3.6 7.5 + - - -
131B GLY* 4.0 3.1 - - - -
155B LYS* 3.3 27.0 + - - +
156B ALA* 3.4 7.6 - - - -
157B ALA* 3.6 26.9 - - - +
187B GLY* 5.1 3.1 - - - -
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Residues in contact with GLY 131 (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 PRO* 3.6 5.5 - - - +
115A VAL* 2.7 42.9 + - - +
129A PHE* 5.7 0.4 - - - -
130A SER* 1.3 76.7 - - - +
132A GLU* 1.3 58.5 + - - +
154A TYR* 5.0 1.6 - - - -
155A LYS 3.2 12.6 - - - -
156A ALA* 3.9 5.6 - - - -
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Residues in contact with GLU 132 (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 GLY* 3.9 28.2 - - - +
113A THR 3.4 3.6 - - - +
114A PRO* 5.9 0.2 - - + -
131A GLY* 1.3 74.1 - - - -
133A ALA* 1.3 67.0 + - - +
134A LEU* 4.0 2.3 - - - +
154A TYR* 3.0 8.2 - - - +
155A LYS* 2.7 56.1 + - + +
155B LYS* 4.9 14.6 - - + +
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Residues in contact with ALA 133 (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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109A MET* 4.8 3.1 - - + -
110A LYS 3.6 11.2 - - - +
111A LYS* 3.7 4.0 - - - +
112A GLY* 2.8 23.1 + - - -
113A THR* 2.7 36.7 + - - +
115A VAL* 3.7 6.3 - - + +
132A GLU* 1.3 75.6 - - - +
134A LEU* 1.3 65.1 + - - +
152A PHE* 3.7 27.6 - - + -
153A ALA 4.1 0.4 - - - -
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Residues in contact with LEU 134 (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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109A MET 5.3 2.1 - - - +
110A LYS 4.9 0.2 - - - -
111A LYS* 3.4 38.1 + - + +
132A GLU* 5.6 1.6 - - - +
133A ALA* 1.3 81.7 - - - +
135A THR* 1.3 74.2 + - + +
137A LYS* 6.2 0.7 - - - -
152A PHE* 4.2 4.1 - - - -
153A ALA* 3.1 21.6 + - + +
154A TYR* 3.8 16.4 - - - +
155A LYS* 3.5 25.4 - - + +
188A VAL* 3.7 30.7 - - + -
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Residues in contact with THR 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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111A LYS* 4.2 20.4 - - + +
134A LEU* 1.3 90.3 - - + +
136A TYR* 1.3 72.2 + - - +
137A LYS* 3.7 17.9 + - - +
152A PHE* 4.3 4.3 - - - -
153A ALA* 3.2 27.3 + - - +
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Residues in contact with TYR 136 (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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74A ILE* 5.2 2.1 - - - +
75A LYS 5.0 7.3 + - - -
76A VAL* 6.1 0.2 - - - -
107A ALA* 4.9 19.7 - - + -
109A MET* 6.2 1.1 - - + -
135A THR* 1.3 83.3 + - - +
137A LYS* 1.3 70.1 + - - +
138A ASP* 3.4 29.0 - - - +
150A GLY* 3.3 28.7 + - - -
151A LEU 3.1 23.3 - - - -
152A PHE* 4.3 8.0 - - + +
193A CYS* 3.9 19.3 - - + -
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Residues in contact with LYS 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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134A LEU* 6.2 0.2 - - - -
135A THR* 3.8 25.6 + - - +
136A TYR* 1.3 83.2 - - - +
138A ASP* 1.3 64.3 + - - +
139A ILE 4.4 4.5 - - - +
140A VAL* 3.7 30.3 - - + -
150A GLY* 3.5 3.3 - - - -
151A LEU* 2.7 42.1 + - + +
153A ALA* 4.5 18.4 - - + -
190A TYR* 4.7 7.4 - - + -
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Residues in contact with ASP 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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76A VAL* 4.2 19.8 - - + +
77A LYS* 4.2 24.5 + - + +
136A TYR* 3.4 27.1 - - - +
137A LYS* 1.3 72.9 - - - +
139A ILE* 1.3 63.9 + - + +
149A PRO* 3.3 7.1 - - - +
150A GLY 2.9 22.6 + - - -
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Residues in contact with ILE 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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76A VAL* 4.6 9.0 - - + -
81A MET* 3.6 22.0 - - - -
137A LYS* 3.4 4.7 - - - +
138A ASP* 1.3 85.2 + - + +
140A VAL* 1.3 70.0 + - - +
141A VAL* 5.1 9.0 - - + +
147A THR* 3.3 37.5 - - + +
148A MET 3.5 6.7 - - - +
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Residues in contact with VAL 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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137A LYS* 3.7 26.2 - - + -
139A ILE* 1.3 81.4 - - - +
141A VAL* 1.3 66.1 + - - +
142A LEU* 3.6 8.9 + - + +
147A THR* 3.7 1.6 - - - -
148A MET* 3.0 28.9 + - - +
151A LEU* 3.3 34.8 - - + -
190A TYR* 4.2 15.3 - - + -
3C PRO* 3.7 29.4 - - + -
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Residues in contact with VAL 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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139A ILE* 5.2 9.9 - - + -
140A VAL* 1.3 76.0 - - - +
142A LEU* 1.3 72.5 + - - +
145A GLY* 4.3 14.4 - - - +
146A ASP 3.6 8.1 - - - +
147A THR* 4.1 13.2 - - - +
2C ALA* 5.5 1.0 - - - +
3C PRO* 3.7 17.2 - - - +
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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