Contacts of the strand formed by residues 139 - 152 (chain A) in PDB entry 4WNB
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A GLN* 4.8 0.7 - - - -
136A THR* 2.6 44.1 + - - -
137A ALA 3.2 1.4 + - - -
138A LEU* 1.3 82.1 - - - +
140A GLU* 1.3 66.5 + - - -
141A GLY 3.5 0.5 + - - -
167A PHE* 4.4 2.1 - - - +
168A LYS 3.6 8.5 - - - -
169A PRO 5.4 0.7 - - - -
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Residues in contact with GLU 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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99A TYR* 3.1 27.8 + - + -
133A PRO* 3.8 22.1 - - + +
134A LYS 3.2 12.3 - - - +
135A GLN* 3.4 32.5 + - - +
139A GLY* 1.3 71.0 - - - -
141A GLY* 1.3 61.5 + - - +
167A PHE* 3.2 1.6 - - - -
168A LYS* 2.8 52.6 + - + +
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Residues in contact with GLY 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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99A TYR* 3.9 5.6 - - - -
132A GLY* 4.2 0.2 - - - -
133A PRO* 3.4 2.6 - - - +
134A LYS* 2.7 42.9 + - - +
139A GLY 3.5 1.2 + - - -
140A GLU* 1.3 77.3 - - - +
142A TRP* 1.3 65.8 + - - -
143A PHE 4.3 0.4 + - - -
165A LEU* 4.0 12.1 - - - -
166A LYS 3.0 13.9 - - - -
167A PHE* 3.9 3.1 - - - -
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Residues in contact with TRP 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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4A VAL* 3.9 27.1 - - + -
7A ILE* 3.9 30.3 - - + -
8A GLN* 4.5 13.7 - - + -
11A VAL* 5.8 0.4 - - + -
94A PHE* 3.3 35.0 - + + -
99A TYR* 3.4 36.7 + + - -
130A VAL* 3.8 26.9 - - + -
131A VAL 3.3 4.3 - - - +
132A GLY* 3.5 31.0 - - - -
133A PRO* 3.5 23.6 - - + +
141A GLY* 1.3 82.0 - - - -
143A PHE* 1.3 61.5 + - - +
144A ILE* 3.7 5.3 + - + +
165A LEU* 3.6 5.2 - - - +
166A LYS* 2.8 32.4 + - - +
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Residues in contact with PHE 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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105A THR* 4.2 3.8 - - + -
129A ASP 3.7 1.7 - - - +
130A VAL* 3.4 3.8 - - - +
131A VAL* 2.8 47.7 + - + +
134A LYS* 4.1 22.0 - - + -
136A THR* 3.9 13.2 - - + -
142A TRP* 1.3 71.2 - - - +
144A ILE* 1.3 60.0 + - - +
145A ASN* 4.2 2.9 + - - +
163A ARG* 4.2 18.2 - - + -
164A ILE 3.4 4.3 - - - +
165A LEU* 3.7 37.2 - - + -
203A 4BN 3.3 86.1 - + + -
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Residues in contact with ILE 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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87A LEU* 6.5 0.2 - - + -
90A ILE* 4.2 17.3 - - + +
94A PHE* 3.5 40.6 - - + -
127A LEU* 4.1 19.7 - - + -
129A ASP 3.9 2.0 - - - -
130A VAL* 4.1 12.8 - - + -
142A TRP 4.1 4.5 - - - +
143A PHE* 1.3 76.3 - - - +
145A ASN* 1.3 73.7 + - - +
146A GLN* 4.1 3.0 + - + +
162A TRP 3.7 0.3 - - - +
163A ARG* 3.2 4.1 - - - +
164A ILE* 2.8 52.6 + - + +
166A LYS* 3.6 26.7 - - + -
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Residues in contact with ASN 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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127A LEU* 3.8 3.1 - - - +
128A GLY* 2.7 31.3 + - - +
129A ASP* 2.8 49.8 + - - +
131A VAL* 5.2 4.0 - - - +
143A PHE* 4.5 4.6 + - - +
144A ILE* 1.3 80.6 - - - +
146A GLN* 1.3 56.8 + - - +
161A ASN* 3.8 17.4 - - - +
162A TRP 3.2 3.4 - - - -
163A ARG* 2.5 48.9 + - - +
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Residues in contact with GLN 146 (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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81A ARG* 4.6 6.1 + - - -
85A ASP* 3.9 4.6 + - - +
86A PRO* 4.2 6.3 - - - +
87A LEU* 3.4 43.0 - - - +
90A ILE* 5.5 0.6 - - - +
125A ALA* 4.2 8.7 - - + +
126A GLU 3.5 13.0 - - - +
127A LEU* 4.9 7.2 - - + +
128A GLY 4.3 0.2 - - - +
144A ILE* 4.1 3.5 + - + +
145A ASN* 1.3 75.7 - - - +
147A HIS* 1.3 62.9 + - - +
148A ILE* 3.5 22.4 - - + +
160A MET 3.6 0.2 - - - +
161A ASN* 3.4 6.2 - - - -
162A TRP* 2.7 71.2 + - + +
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Residues in contact with HIS 147 (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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124A SER 3.9 0.7 - - - +
125A ALA* 3.5 1.2 - - - -
126A GLU* 2.8 56.4 + - + +
127A LEU 5.5 0.2 - - - -
128A GLY* 4.7 7.4 - - - +
146A GLN* 1.3 74.8 - - - +
148A ILE* 1.3 62.2 + - - +
149A VAL* 3.3 30.6 - - + +
159A GLU* 3.7 15.7 + - - -
160A MET 3.5 4.3 - - - -
161A ASN* 3.9 20.2 - - - +
201A CD 2.6 30.0 - - - -
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Residues in contact with ILE 148 (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 ILE* 3.5 36.3 - - + -
124A SER 3.4 2.0 - - - +
125A ALA* 3.4 29.8 - - + -
146A GLN* 3.5 21.5 - - + +
147A HIS* 1.3 78.5 + - - +
149A VAL* 1.3 66.1 + - - +
150A TRP* 3.7 21.1 - - + -
159A GLU* 3.1 9.2 - - - +
160A MET* 2.7 64.0 + - + +
162A TRP* 4.4 6.5 - - + +
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Residues in contact with VAL 149 (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 SER 3.8 0.5 - - - +
123A ILE* 3.5 3.6 - - - +
124A SER* 2.9 41.6 + - - +
147A HIS* 3.3 33.9 - - + +
148A ILE* 1.3 74.6 - - - +
150A TRP* 1.3 70.3 + - - +
151A GLN* 4.1 20.4 + - + +
156A ASP* 3.7 27.8 - - + +
158A ALA 3.6 2.0 - - - -
159A GLU* 4.4 5.8 - - + +
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Residues in contact with TRP 150 (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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69A ILE* 3.4 40.7 + - + -
70A GLN* 3.7 31.6 - - + -
73A THR* 3.0 23.4 + - + -
109A GLN* 4.3 2.2 - - - -
121A VAL* 3.3 30.5 - - + -
122A SER 3.2 9.0 - - - +
123A ILE* 3.8 13.7 - - + +
148A ILE* 3.7 16.8 - - + -
149A VAL* 1.3 73.0 - - - +
151A GLN* 1.3 64.2 + - - +
156A ASP* 3.7 1.9 - - - +
157A VAL* 2.9 28.2 + - + +
158A ALA* 2.8 32.3 + - + +
159A GLU* 3.7 10.1 - - - -
160A MET* 3.6 45.5 - - + -
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Residues in contact with GLN 151 (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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22A PRO* 4.7 15.4 - - - +
120A GLN 3.8 0.5 - - - +
121A VAL* 3.3 6.1 - - - -
122A SER* 2.9 42.7 + - - +
124A SER* 5.0 10.3 - - - +
149A VAL* 4.1 19.1 + - + +
150A TRP* 1.3 79.2 - - - +
152A VAL* 1.3 63.9 + - - +
153A GLY 3.4 21.7 + - - +
154A ASP* 3.6 20.5 - - - +
155A GLU 3.0 14.4 - - - +
156A ASP* 4.3 3.4 - - - -
157A VAL* 4.2 2.2 - - - -
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Residues in contact with VAL 152 (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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113A ARG* 3.9 15.5 - - - +
115A LEU* 4.1 13.0 - - + -
119A GLU* 4.0 30.1 - - + +
120A GLN 3.7 18.4 - - - +
121A VAL* 4.4 7.2 - - + -
151A GLN* 1.3 73.0 - - - +
153A GLY* 1.3 64.9 + - - +
154A ASP 3.2 0.5 + - - -
155A GLU* 2.9 26.3 + - - +
157A VAL* 3.8 21.1 - - + +
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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