Contacts of the strand formed by residues 97 - 108 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B GLU* 4.0 35.2 - - + +
192B THR* 4.5 10.1 - - + -
193B VAL 3.6 9.0 - - - +
194B THR* 4.5 9.0 - - + -
95C GLU 4.0 8.3 - - - +
96C MET* 1.3 77.2 - - - +
98C VAL* 1.3 64.1 + - - +
99C VAL* 4.2 9.3 - - + +
121C ILE 3.8 0.5 - - - +
122C GLY* 3.3 3.8 - - - -
123C TYR* 2.9 68.3 + - + +
125C PRO* 4.7 4.9 - - + -
129C ILE* 5.0 2.9 - - + -
132C LEU* 4.7 2.5 - - + -
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Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ARG 3.9 0.9 - - - +
192B THR* 3.3 4.2 - - - +
193B VAL* 2.7 52.5 + - + +
96C MET* 3.8 29.2 - - + +
97C VAL* 1.3 78.1 - - - +
99C VAL* 1.3 67.1 + - - +
100C LYS* 4.4 13.9 - - + -
121C ILE 3.3 8.5 - - - +
211C PHE* 4.1 21.8 - - + -
214C HIS* 4.2 21.5 - - + -
215C LEU* 4.2 17.0 - - + -
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B MET* 5.2 4.3 - - + -
190B SER* 3.6 20.6 - - - +
191B ARG 3.7 2.9 - - - -
192B THR* 4.1 9.6 - - + +
97C VAL* 4.6 5.4 - - + -
98C VAL* 1.3 74.0 - - - +
100C LYS* 1.3 58.9 + - - +
102C VAL* 3.8 15.1 - - + +
119C VAL 4.1 2.3 - - - +
120C HIS* 3.6 1.9 - - - -
121C ILE* 2.7 44.1 + - + +
123C TYR* 5.7 0.7 - - + -
132C LEU* 3.9 26.7 - - + +
135C PHE* 3.9 38.4 - - + -
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Residues in contact with LYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU* 2.9 29.7 + - - -
189B HIS 4.7 0.2 - - - -
190B SER* 3.1 8.7 + - - -
191B ARG* 2.9 68.2 + - + +
193B VAL* 3.8 15.1 - - + +
98C VAL* 4.4 10.5 - - + +
99C VAL* 1.3 74.3 - - - +
101C GLY* 1.3 62.2 + - - +
102C VAL 3.4 3.1 - - - -
120C HIS* 3.4 17.7 - - + +
214C HIS* 2.9 30.4 + - - +
215C LEU* 4.0 20.4 - - + +
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Residues in contact with GLY 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B HIS* 3.0 35.0 - - - +
190B SER* 3.1 1.9 + - - -
100C LYS* 1.3 74.5 - - - +
102C VAL* 1.3 60.4 + - - +
103C GLU 3.1 7.3 + - - -
118C LYS* 3.7 24.5 - - - -
119C VAL 3.6 0.2 + - - -
120C HIS* 3.0 20.1 + - - -
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Residues in contact with VAL 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B MET* 5.4 1.1 - - + -
187B LYS* 4.0 9.2 - - + -
190B SER* 3.7 22.7 - - - +
99C VAL* 3.8 20.6 - - + +
100C LYS 4.4 0.4 - - - +
101C GLY* 1.3 74.4 - - - +
103C GLU* 1.3 74.2 + - - +
118C LYS* 4.1 0.2 - - - -
119C VAL* 2.8 46.7 + - + +
121C ILE* 5.4 2.5 - - + -
135C PHE* 5.4 2.2 - - + -
136C ALA* 3.9 37.7 - - + +
139C VAL* 4.1 15.7 - - + -
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLU 4.4 1.2 - - - +
187B LYS* 2.8 45.6 + - + +
188B GLN* 2.8 33.8 + - - +
189B HIS* 3.0 43.2 + - + +
101C GLY 3.1 4.5 + - - +
102C VAL* 1.3 77.6 - - - +
104C PHE* 1.3 61.2 + - - +
105C TYR* 4.5 20.4 - - + +
117C GLY 3.2 13.0 - - - +
118C LYS* 4.1 3.6 - - + +
139C VAL* 4.5 0.3 - - - +
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Residues in contact with PHE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B LYS* 4.6 3.6 - - - +
103C GLU* 1.3 77.0 - - - +
105C TYR* 1.3 79.3 + - - +
106C SER* 4.3 1.3 - - - -
115C PHE* 3.7 32.3 - + - -
116C PHE* 3.1 26.3 - - - +
117C GLY* 3.0 38.5 + - - +
118C LYS 3.4 12.3 - - - -
119C VAL* 3.6 16.6 - - + -
139C VAL* 3.7 23.3 - - + -
140C ASP* 5.1 2.0 - - - +
143C ALA* 4.3 6.1 - - + -
149C GLN* 5.1 0.2 - - + -
152C LEU* 3.6 24.0 - - + -
173C VAL* 3.6 26.9 - - + -
174C GLU 3.8 3.8 - - - -
175C GLY* 4.5 3.1 - - - -
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Residues in contact with TYR 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B LYS* 5.8 2.7 - - - -
72C LEU* 6.3 3.6 - - + -
103C GLU* 4.5 21.4 - - + +
104C PHE* 1.3 83.7 - - - +
106C SER* 1.3 60.9 + - - +
114C PRO* 6.0 3.8 - - + -
115C PHE 3.8 4.0 - - - -
116C PHE* 3.4 40.6 - + + -
140C ASP* 5.7 0.8 + - - -
143C ALA* 3.4 20.5 - - - +
144C ARG* 4.4 7.3 + - - +
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PHE* 4.3 5.2 - - - -
105C TYR* 1.3 74.4 - - - +
107C MET* 1.3 71.5 + - - +
114C PRO* 3.1 9.5 - - - +
115C PHE* 2.9 50.6 + - - -
143C ALA* 2.8 27.2 + - - -
144C ARG* 5.6 0.2 - - - +
145C ARG 3.4 6.6 + - - -
147C GLN* 3.5 18.6 - - - +
152C LEU* 4.8 1.1 - - - -
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Residues in contact with MET 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TRP* 3.7 28.9 - - + +
72C LEU* 3.6 37.5 - - + +
106C SER* 1.3 81.4 + - - +
108C CYS* 1.3 58.5 + - - +
112C LEU 3.7 12.1 - - - +
113C LEU 3.5 5.8 - - - -
114C PRO* 3.4 39.3 - - + -
115C PHE* 3.7 3.5 - - - -
145C ARG 3.7 7.5 + - - +
146C LEU* 3.5 20.0 - - + -
147C GLN* 2.7 33.6 + - - +
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Residues in contact with CYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C MET* 1.3 71.9 - - - +
109C GLU* 1.3 58.6 + - - +
110C HIS 3.1 0.9 - - - +
111C HIS* 3.2 20.6 - - - -
112C LEU* 2.7 36.2 + - - +
113C LEU 2.9 22.1 + - - +
115C PHE* 3.5 14.3 - - + -
147C GLN 3.4 7.2 - - - +
177C HIS* 5.2 0.7 - - - +
179C CYS* 4.1 6.3 - - - -
1003C ZN 2.3 36.6 - - - -
823D 8DG 3.6 17.5 - - - +
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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