Contacts of the strand formed by residues 97 - 108 (chain E) in PDB entry 1WUR
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 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D GLU* 3.9 37.2 - - + +
192D THR* 4.3 14.8 - - + -
193D VAL 3.6 8.7 - - - +
194D THR* 4.4 4.5 - - + -
95E GLU 4.1 8.1 - - - +
96E MET* 1.3 76.2 - - - +
98E VAL* 1.3 63.1 + - - +
99E VAL* 4.5 9.4 - - + -
121E ILE 3.9 0.7 - - - +
122E GLY* 3.3 3.6 - - - -
123E TYR* 2.8 65.2 + - + +
125E PRO* 4.6 7.4 - - + -
129E ILE* 4.9 0.2 - - + -
132E LEU* 4.6 2.9 - - + -
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Residues in contact with VAL 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D THR* 3.3 4.5 - - - +
193D VAL* 2.8 51.2 + - + +
96E MET* 3.8 28.0 - - + -
97E VAL* 1.3 78.8 - - - +
99E VAL* 1.3 68.4 + - - +
100E LYS* 3.9 11.5 + - + +
121E ILE 3.3 10.5 - - - +
211E PHE* 4.0 20.6 - - + -
214E HIS* 4.1 21.3 - - + -
215E LEU* 4.1 17.5 - - + -
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Residues in contact with VAL 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D MET* 5.1 5.4 - - + -
190D SER* 3.6 20.9 - - - +
191D ARG 3.8 2.9 - - - -
192D THR* 3.9 17.9 - - + +
97E VAL* 4.5 5.4 - - + -
98E VAL* 1.3 72.8 - - - +
100E LYS* 1.3 60.4 + - - +
102E VAL* 3.8 15.4 - - + +
119E VAL 4.1 2.3 - - - +
120E HIS* 3.6 1.6 - - - -
121E ILE* 2.8 43.2 + - + +
123E TYR* 5.8 0.4 - - + -
132E LEU* 3.9 18.8 - - + +
135E PHE* 3.9 36.8 - - + -
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Residues in contact with LYS 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLU* 2.9 31.1 + - - -
190D SER* 2.9 21.3 + - - -
191D ARG* 3.0 51.8 + - + +
193D VAL* 3.9 16.2 - - - +
98E VAL* 4.4 9.9 - - + +
99E VAL* 1.3 72.8 - - - +
101E GLY* 1.3 62.3 + - - +
102E VAL 3.4 2.5 - - - -
120E HIS* 3.4 17.5 - - + +
214E HIS* 2.7 31.0 + - - +
215E LEU* 3.9 20.8 - - + +
216E ARG 5.9 0.2 + - - -
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Residues in contact with GLY 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D HIS* 3.0 36.7 - - - +
190D SER* 3.1 1.4 + - - -
191D ARG* 6.4 0.2 - - - -
100E LYS* 1.3 73.0 - - - +
102E VAL* 1.3 59.3 + - - +
103E GLU* 3.1 8.4 + - - +
118E LYS* 3.9 23.1 - - - -
120E HIS* 3.0 19.5 + - - -
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D MET* 5.4 1.8 - - + -
187D LYS* 4.0 12.6 - - + -
190D SER* 3.8 22.4 - - - +
99E VAL* 3.8 20.6 - - + +
100E LYS 4.4 0.4 - - - +
101E GLY* 1.3 74.6 - - - +
103E GLU* 1.3 70.8 + - - +
104E PHE 3.5 0.7 + - - -
118E LYS* 4.2 0.2 - - - -
119E VAL* 2.8 45.1 + - + +
121E ILE* 5.1 5.2 - - + -
136E ALA* 4.0 32.3 - - + +
139E VAL* 4.0 16.8 - - + -
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Residues in contact with GLU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D GLU 4.2 1.4 - - - +
187D LYS* 2.8 47.9 + - + +
188D GLN* 2.7 34.2 + - - +
189D HIS* 3.0 44.3 + - + +
101E GLY 3.1 5.2 + - - +
102E VAL* 1.3 76.4 - - - +
104E PHE* 1.3 59.9 + - - +
105E TYR* 4.5 20.0 - - + +
117E GLY 3.2 12.8 - - - +
118E LYS* 4.2 3.4 - - + +
140E ASP* 4.6 0.2 - - - +
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Residues in contact with PHE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LYS* 4.6 3.8 - - - +
103E GLU* 1.3 75.4 - - - +
105E TYR* 1.3 77.9 + - - +
106E SER* 4.2 1.8 - - - -
115E PHE* 3.6 41.5 - + - -
116E PHE* 3.1 10.5 - - - +
117E GLY* 3.0 57.6 + - - +
118E LYS 3.5 11.7 - - - -
119E VAL* 3.6 15.9 - - + -
139E VAL* 3.7 22.9 - - + -
140E ASP* 5.1 1.3 - - - +
143E ALA* 4.2 6.7 - - + -
149E GLN* 5.0 0.2 - - - -
152E LEU* 3.7 15.5 - - + -
173E VAL* 3.5 27.8 - - + -
174E GLU 3.8 3.8 - - - -
175E GLY* 4.5 2.7 - - - -
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Residues in contact with TYR 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LYS* 5.7 3.1 - - - -
189D HIS* 5.9 2.8 - - - -
72E LEU* 6.1 6.6 - - + +
103E GLU* 4.5 21.7 - - + +
104E PHE* 1.3 84.2 - - - +
106E SER* 1.3 60.3 + - - +
114E PRO* 6.0 4.5 - - + -
115E PHE 3.8 4.7 - - - -
116E PHE* 3.4 40.4 - + + -
140E ASP* 5.7 0.8 + - - -
143E ALA* 3.4 20.4 - - - +
144E ARG* 4.4 6.9 + - - +
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 4.2 4.9 - - - -
105E TYR* 1.3 73.6 - - - +
107E MET* 1.3 70.8 + - - +
114E PRO* 3.2 10.2 - - - +
115E PHE* 2.9 49.7 + - - -
143E ALA* 2.7 28.9 + - - -
145E ARG 3.4 6.4 + - - -
147E GLN* 3.5 18.5 - - - +
152E LEU* 4.8 0.7 - - - -
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Residues in contact with MET 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E TRP* 3.7 28.9 - - + +
72E LEU* 3.6 39.5 - - + +
106E SER* 1.3 81.4 + - - +
108E CYS* 1.3 57.8 + - - +
112E LEU 3.6 12.6 - - - +
113E LEU 3.5 5.2 - - - -
114E PRO* 3.5 38.4 - - + -
115E PHE* 3.8 3.1 - - - -
145E ARG 3.7 6.5 + - - +
146E LEU* 3.4 20.0 - - + -
147E GLN* 2.7 33.1 + - - -
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Residues in contact with CYS 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A 8DG 3.6 17.9 - - + +
107E MET* 1.3 72.1 - - - +
109E GLU* 1.3 56.8 + - - +
110E HIS 3.1 2.9 - - - +
111E HIS* 3.3 14.8 - - - -
112E LEU* 2.9 31.9 + - - +
113E LEU 2.9 29.5 + - - +
115E PHE* 3.6 13.6 - - + -
147E GLN 3.4 7.0 - - - -
177E HIS* 5.3 0.7 - - - +
179E CYS* 4.1 6.5 - - - -
1005E ZN 2.5 36.8 - - - -
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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