Contacts of the strand formed by residues 97 - 108 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C GLU* 3.7 37.7 - - + +
192C THR* 4.3 15.7 - - + -
193C VAL 3.6 9.2 - - - +
194C THR* 4.4 4.9 - - + -
95D GLU 4.3 7.2 - - - +
96D MET* 1.3 76.7 - - - +
98D VAL* 1.3 63.9 + - - +
99D VAL* 4.3 11.2 - - + +
121D ILE 3.8 0.9 - - - +
122D GLY* 3.3 3.3 - - - -
123D TYR* 2.8 65.0 + - + +
125D PRO* 4.9 4.0 - - + -
129D ILE* 5.1 2.5 - - + -
132D LEU* 4.6 2.7 - - + -
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Residues in contact with VAL 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C ARG 3.9 0.2 - - - +
192C THR* 3.3 3.6 - - - +
193C VAL* 2.7 53.2 + - + +
96D MET* 3.8 29.2 - - + +
97D VAL* 1.3 78.5 - - - +
99D VAL* 1.3 63.6 + - - +
100D LYS* 3.9 15.3 + - + +
121D ILE 3.3 7.9 - - - +
211D PHE* 4.1 22.4 - - + -
214D HIS* 4.3 19.5 - - + +
215D LEU* 4.1 18.2 - - + -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C MET* 5.1 4.0 - - + -
190C SER* 3.7 20.6 - - - +
191C ARG 3.7 2.7 - - - -
192C THR* 4.0 12.3 - - + +
97D VAL* 4.3 6.3 - - + -
98D VAL* 1.3 74.1 - - - +
100D LYS* 1.3 59.3 + - - +
102D VAL* 3.9 13.9 - - + +
119D VAL 4.1 2.3 - - - +
120D HIS* 3.6 1.7 - - - -
121D ILE* 2.7 42.4 + - + +
123D TYR* 5.7 0.4 - - + -
132D LEU* 3.8 33.2 - - + +
135D PHE* 3.9 31.9 - - + -
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Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLU* 3.0 31.2 + - - -
190C SER* 3.0 9.4 + - - -
191C ARG* 2.9 60.7 + - + +
193C VAL* 3.8 18.6 - - - +
98D VAL* 4.4 9.9 - - + +
99D VAL* 1.3 73.9 - - - +
101D GLY* 1.3 61.9 + - - +
102D VAL 3.4 2.9 - - - -
120D HIS* 3.3 18.6 - - + +
214D HIS* 2.9 31.7 + - - +
215D LEU* 3.9 19.3 - - + -
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C HIS* 3.0 36.7 - - - +
190C SER* 3.1 2.3 + - - -
191C ARG* 6.2 1.1 - - - -
100D LYS* 1.3 72.9 - - - +
102D VAL* 1.3 60.5 + - - +
103D GLU 3.1 7.4 + - - -
118D LYS* 4.0 15.7 - - - -
119D VAL 3.6 0.6 + - - -
120D HIS* 3.0 25.9 + - - -
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Residues in contact with VAL 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C MET* 5.2 2.2 - - + -
187C LYS* 4.0 11.9 - - + -
190C SER* 3.7 22.9 - - - +
99D VAL* 3.9 21.1 - - + +
100D LYS 4.4 0.9 - - - +
101D GLY* 1.3 73.1 - - - +
103D GLU* 1.3 71.7 + - - +
104D PHE 3.6 0.2 + - - -
118D LYS* 4.1 0.4 - - - -
119D VAL* 2.7 46.2 + - + +
121D ILE* 5.5 2.0 - - + -
135D PHE* 5.4 2.2 - - + -
136D ALA* 4.0 33.7 - - + +
139D VAL* 4.0 15.9 - - + -
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C GLU 4.4 0.9 - - - +
187C LYS* 2.9 48.7 + - + +
188C GLN* 2.7 34.4 + - - +
189C HIS* 3.0 44.3 + - + +
190C SER 4.2 0.2 + - - -
101D GLY 3.1 4.6 + - - +
102D VAL* 1.3 76.1 - - - +
104D PHE* 1.3 59.2 + - - +
105D TYR* 4.5 20.4 - - + +
117D GLY 3.2 13.0 - - - +
118D LYS* 4.2 3.1 - - + +
139D VAL* 4.6 0.3 - - - +
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Residues in contact with PHE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LYS* 4.8 2.5 - - - +
103D GLU* 1.3 75.8 - - - +
105D TYR* 1.3 76.5 + - - +
106D SER* 4.2 2.2 - - - -
115D PHE* 3.6 42.2 - + - -
116D PHE* 3.2 12.4 - - - +
117D GLY* 2.9 55.6 + - - +
118D LYS 3.5 11.0 - - - -
119D VAL* 3.6 17.0 - - + -
139D VAL* 3.7 23.3 - - + -
140D ASP* 5.1 1.6 - - - -
143D ALA* 4.3 5.6 - - + -
149D GLN* 5.0 0.2 - - - -
152D LEU* 3.7 14.8 - - + -
173D VAL* 3.4 28.3 - - + -
174D GLU 3.8 2.9 - - - -
175D GLY* 4.5 4.7 - - - -
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Residues in contact with TYR 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LYS* 5.8 3.1 - - - -
72D LEU* 6.2 4.4 - - + +
103D GLU* 4.5 22.0 - - + +
104D PHE* 1.3 82.2 - - - +
106D SER* 1.3 59.8 + - - +
114D PRO* 6.1 4.3 - - + -
115D PHE 3.8 3.6 - - - -
116D PHE* 3.4 36.6 - + + -
140D ASP* 5.6 1.0 + - - -
143D ALA* 3.4 19.7 - - - +
144D ARG* 4.4 8.1 + - - +
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 4.3 5.2 - - - -
105D TYR* 1.3 74.0 - - - +
107D MET* 1.3 70.8 + - - +
114D PRO* 3.1 10.1 - - - +
115D PHE* 2.9 52.0 + - - +
143D ALA* 2.7 30.0 + - - -
145D ARG 3.4 6.1 + - - -
147D GLN* 3.5 17.5 - - - +
152D LEU* 4.8 0.9 - - - -
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Residues in contact with MET 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TRP* 3.6 28.7 - - + +
72D LEU* 3.6 38.1 - - + +
106D SER* 1.3 80.0 + - - +
108D CYS* 1.3 60.6 + - - +
112D LEU 3.6 14.4 - - - +
113D LEU 3.6 5.6 - - - -
114D PRO* 3.5 37.9 - - + -
115D PHE* 3.6 4.8 - - - -
145D ARG 3.7 10.9 + - - +
146D LEU* 3.5 15.7 - - + -
147D GLN 2.7 27.5 + - - +
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Residues in contact with CYS 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D MET* 1.3 70.7 - - - +
109D GLU* 1.3 58.6 + - - +
110D HIS 4.2 0.2 - - - +
111D HIS* 3.2 19.5 - - - -
112D LEU* 2.7 36.5 + - - +
113D LEU 2.9 23.9 + - - +
115D PHE* 3.6 14.1 - - + -
147D GLN 3.3 6.1 - - - +
177D HIS* 5.1 1.1 - - - +
179D CYS* 4.1 5.2 - - - -
824D 8DG 3.6 18.2 - - + +
1004D ZN 2.4 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