Contacts of the strand formed by residues 121 - 136 (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 VAL 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.7 6.2 - - - +
25A ALA* 2.9 36.3 + - + +
27A ASP 5.3 0.2 + - - -
29A VAL* 4.3 12.5 - - + +
69A ILE* 4.1 6.3 - - + +
72A TRP* 4.5 8.7 - - + -
73A THR* 4.2 4.3 - - + -
115A LEU* 3.5 31.9 - - + -
120A GLN* 1.3 78.6 - - - +
122A SER* 1.3 65.7 + - - +
150A TRP* 3.3 41.5 - - + -
151A GLN 3.3 6.3 - - - +
152A VAL* 4.4 9.0 - - + -
157A VAL* 5.2 0.7 - - + -
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Residues in contact with SER 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 4.0 22.8 - - - +
23A ARG 3.2 14.1 - - - -
24A LEU* 4.2 12.3 - - - -
25A ALA 4.6 0.2 - - - +
73A THR* 4.4 0.4 - - - -
121A VAL* 1.3 80.9 - - - +
123A ILE* 1.3 61.1 + - - +
150A TRP* 3.2 7.7 - - - -
151A GLN* 2.9 50.8 + - - +
153A GLY 4.6 4.4 + - - -
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Residues in contact with ILE 123 (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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20A SER* 4.4 1.6 + - - -
21A LYS 4.1 1.7 - - - +
22A PRO* 3.4 3.8 - - - +
23A ARG* 2.9 78.2 + - - +
70A GLN* 6.0 0.9 - - + -
73A THR* 3.7 23.3 - - + +
122A SER* 1.3 77.1 - - - +
124A SER* 1.3 66.1 + - - +
125A ALA* 5.0 2.2 - - + +
148A ILE* 3.5 34.5 - - + -
149A VAL 3.5 2.5 - - - -
150A TRP* 3.8 15.7 - - + +
151A GLN* 6.3 0.2 - - - -
160A MET* 6.1 0.7 - - + -
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Residues in contact with SER 124 (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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19A PRO* 3.6 14.8 - - - +
20A SER* 2.5 30.0 + - - -
22A PRO* 4.6 13.4 - - - +
123A ILE* 1.3 78.9 - - - +
125A ALA* 1.3 60.0 + - - +
147A HIS 3.9 0.7 - - - +
148A ILE* 3.4 4.0 - - - +
149A VAL* 2.9 40.0 + - - +
151A GLN* 5.0 10.3 - - - +
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Residues in contact with ALA 125 (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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19A PRO* 3.3 4.7 - - - +
20A SER* 2.8 35.3 + - - +
85A ASP* 4.1 24.7 - - - +
86A PRO* 3.7 9.7 - - + +
123A ILE* 5.6 3.6 - - + -
124A SER* 1.3 74.2 + - - +
126A GLU* 1.3 60.2 + - - +
146A GLN* 4.2 5.8 - - - +
147A HIS 3.5 4.3 - - - -
148A ILE* 3.4 22.0 - - + -
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Residues in contact with GLU 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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15A LYS* 5.4 5.7 - - + +
18A GLY* 4.7 4.9 - - - -
19A PRO* 4.1 37.7 - - + +
86A PRO* 4.0 7.4 - - - -
125A ALA* 1.3 76.2 - - - +
127A LEU* 1.3 69.7 + - - +
146A GLN* 3.5 4.6 - - - +
147A HIS* 2.8 50.5 + - + +
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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
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11A VAL* 3.8 23.3 - - + +
14A ILE* 4.0 14.6 - - + -
15A LYS* 3.9 29.6 - - + +
86A PRO* 3.9 21.4 - - + +
90A ILE* 3.6 47.6 - - + -
126A GLU* 1.3 85.8 - - - +
128A GLY* 1.3 66.8 + - - +
130A VAL* 4.2 3.6 - - + -
144A ILE* 4.1 16.4 - - + -
145A ASN 4.0 3.4 - - - +
146A GLN* 4.9 8.1 - - - +
147A HIS* 5.5 0.7 - - - -
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Residues in contact with GLY 128 (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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15A LYS* 3.0 26.1 - - - -
126A GLU 3.6 2.2 + - - -
127A LEU* 1.3 70.7 - - - +
129A ASP* 1.3 66.1 + - - -
130A VAL* 3.5 5.2 + - - +
145A ASN* 2.7 22.5 + - - -
146A GLN* 4.3 0.4 - - - +
147A HIS* 5.3 7.2 - - - -
161A ASN* 6.0 1.6 - - - -
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Residues in contact with ASP 129 (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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15A LYS* 4.3 6.6 + - - +
128A GLY* 1.3 71.4 - - - -
130A VAL* 1.3 58.8 + - - +
131A VAL* 4.1 13.2 - - + -
143A PHE 3.7 0.5 - - - +
145A ASN* 2.8 51.5 + - - +
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Residues in contact with VAL 130 (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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11A VAL* 3.8 37.0 - - + -
15A LYS* 4.5 3.0 - - - +
90A ILE* 4.6 1.3 - - + -
94A PHE* 3.9 17.7 - - + -
127A LEU* 4.2 14.6 - - + -
128A GLY 3.5 7.9 + - - +
129A ASP* 1.3 78.7 - - - +
131A VAL* 1.3 63.6 + - - +
132A GLY 4.3 0.5 + - - -
142A TRP* 3.8 26.6 - - + -
143A PHE 3.4 2.9 - - - +
144A ILE* 4.1 24.0 - - + -
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Residues in contact with VAL 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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129A ASP* 4.4 18.2 - - + -
130A VAL* 1.3 79.9 - - - +
132A GLY* 1.3 60.0 + - - +
134A LYS* 3.8 28.7 - - + -
142A TRP* 3.3 6.2 - - - -
143A PHE* 2.8 53.1 + - + +
145A ASN* 5.2 2.9 - - - +
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Residues in contact with GLY 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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4A VAL* 5.1 1.2 - - - +
8A GLN* 5.1 3.5 + - - -
131A VAL* 1.3 82.6 - - - +
133A PRO* 1.3 75.9 - - - +
134A LYS* 3.9 4.7 - - - -
142A TRP* 3.5 27.0 - - - -
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Residues in contact with PRO 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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4A VAL* 4.4 19.1 - - + -
99A TYR* 4.0 2.0 - - - +
132A GLY* 1.3 84.4 - - - +
134A LYS* 1.3 62.8 + - - +
135A GLN* 4.6 5.4 + - - +
140A GLU* 3.8 31.6 - - + +
141A GLY 3.4 5.2 - - - +
142A TRP* 3.5 30.0 - - + +
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Residues in contact with LYS 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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131A VAL* 3.8 24.0 - - + -
132A GLY* 4.5 5.8 - - - -
133A PRO* 1.3 78.4 - - - +
135A GLN* 1.3 67.7 + - - +
136A THR* 3.7 4.7 + - + +
140A GLU* 3.2 4.0 - - - -
141A GLY* 2.7 38.6 + - - +
143A PHE* 4.1 24.2 - - + -
203A 4BN 3.2 64.6 + - + +
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Residues in contact with GLN 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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133A PRO* 4.6 5.1 + - - +
134A LYS* 1.3 81.2 - - - +
136A THR* 1.3 62.4 + - - +
139A GLY 4.4 1.7 - - - -
140A GLU* 3.4 36.4 + - - +
203A 4BN 3.9 26.8 + - - +
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Residues in contact with THR 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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134A LYS 3.9 8.5 - - - +
135A GLN* 1.3 79.3 - - - +
137A ALA* 1.3 57.1 + - - +
138A LEU 3.3 10.0 + - - -
139A GLY* 2.6 45.7 + - - +
143A PHE* 3.9 32.1 - - + -
165A LEU* 3.7 19.9 - - + +
203A 4BN 3.1 26.7 - - - +
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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