Contacts of the strand formed by residues 128 - 138 (chain F) in PDB entry 4WFH
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 128 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123F GLN* 3.4 30.1 + - - +
124F LEU* 3.5 13.9 - - - +
126F SER* 3.5 4.2 + - - -
127F GLY* 1.3 79.9 - - - +
129F ALA* 1.3 63.4 + - - +
179F THR* 6.4 0.4 - - - -
180F LEU 4.0 5.4 - - - -
181F THR* 4.8 0.4 - - - -
182F LYS 4.3 1.1 - - - -
146G LYS* 6.4 0.2 - - - -
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Residues in contact with ALA 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F PRO* 4.0 9.9 - - + -
123F GLN* 3.5 6.6 - - - +
124F LEU* 3.8 14.4 - - + -
128F GLY* 1.3 74.8 - - - +
130F SER* 1.3 62.7 + - - +
131F VAL* 4.0 1.4 + - - +
178F LEU 3.7 1.6 - - - +
179F THR* 5.4 0.6 - - - +
180F LEU* 2.8 44.1 + - - +
181F THR 4.2 0.7 - - - +
182F LYS* 4.2 4.7 - - - -
185F TYR* 3.7 30.5 - - + -
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Residues in contact with SER 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F PHE 4.3 1.0 - - - +
118F PRO 4.3 0.3 - - - -
119F PRO* 3.6 20.6 - - - +
123F GLN* 3.0 26.2 + - - +
129F ALA* 1.3 72.5 - - - +
131F VAL* 1.3 63.7 + - - +
132F VAL* 4.0 5.3 + - - +
177F THR* 4.2 11.1 - - - +
178F LEU 3.3 6.3 - - - -
179F THR* 3.6 22.2 + - - +
127G LEU* 5.4 2.9 - - - +
144G LEU* 3.7 22.6 - - - +
146G LYS* 3.9 7.6 + - - +
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Residues in contact with VAL 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 4.2 2.2 - - + -
117F PHE 3.3 17.3 - - - +
119F PRO* 4.0 16.6 - - + -
129F ALA 4.7 3.4 - - - +
130F SER* 1.3 75.5 - - - +
132F VAL* 1.3 61.1 + - - +
147F TRP* 3.6 30.9 - - + -
177F THR* 3.4 2.1 - - - -
178F LEU* 2.6 51.5 + - + +
180F LEU* 4.8 2.9 - - + -
185F TYR* 4.6 8.3 - - + -
191F TYR* 4.6 19.5 - - + -
208F PHE* 3.7 22.2 - - + -
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Residues in contact with VAL 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F ILE* 3.4 2.9 - - - +
117F PHE* 2.7 46.6 + - + -
130F SER 4.4 6.7 - - - +
131F VAL* 1.3 79.9 - - - +
133F CYS* 1.3 64.1 + - - +
134F PHE* 3.3 33.9 - - + -
147F TRP* 4.0 2.2 - - - -
175F SER* 5.2 1.6 - - - -
176F SER 3.5 6.3 - - - +
177F THR* 4.0 22.0 - - + +
127G LEU* 4.0 30.5 - - + -
144G LEU* 4.5 15.0 - - + -
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Residues in contact with CYS 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F VAL* 3.7 17.3 - - - -
115F SER 3.1 16.2 - - - -
116F ILE* 4.4 1.6 - - - -
132F VAL* 1.3 74.9 - - - +
134F PHE* 1.3 64.1 + - - +
135F LEU* 3.8 8.2 - - + +
147F TRP* 3.7 14.4 - - + -
175F SER* 3.3 4.3 - - - -
176F SER* 2.8 39.3 + - - +
193F CYS* 2.0 51.1 - - - -
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Residues in contact with PHE 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F THR 3.3 2.0 - - - +
114F VAL* 3.3 7.6 - - - +
115F SER* 2.8 39.9 + - - +
117F PHE* 3.6 21.1 - + - -
132F VAL* 3.3 21.5 - - + -
133F CYS* 1.3 79.5 - - - +
135F LEU* 1.3 61.6 + - - +
136F ASN* 3.6 21.8 - - - +
174F MET 3.7 2.0 - - - -
175F SER* 4.1 13.7 - - - -
127G LEU* 3.9 19.5 - - + -
140G THR* 3.9 14.1 - - + -
141G LEU 4.2 5.2 - - - -
142G GLY* 4.1 17.5 - - - -
143G CYS 5.2 3.4 - - - -
169G PHE* 4.1 23.1 - + - -
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F PRO* 4.2 10.3 - - + -
113F THR 3.6 3.4 - - - -
114F VAL* 4.3 10.3 - - + -
133F CYS* 3.8 26.7 - - + +
134F PHE* 1.3 78.3 - - - +
136F ASN* 1.3 59.8 + - - +
138F PHE* 3.2 10.2 - - + -
143F ILE* 3.6 17.0 - - + -
145F VAL* 3.3 36.1 - - + -
173F SER* 3.2 4.2 - - - -
174F MET* 2.8 53.2 + - + +
176F SER* 4.8 2.5 - - - +
193F CYS* 5.6 0.2 - - - -
195F ALA* 3.5 25.4 - - + -
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Residues in contact with ASN 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F PRO* 3.7 0.5 - - - +
113F THR* 2.9 45.9 + - - +
134F PHE* 3.6 27.3 - - - +
135F LEU* 1.3 80.7 + - - +
137F ASN* 1.3 81.3 + - - +
138F PHE* 3.5 2.6 + - - -
173F SER* 3.7 8.2 - - - -
140G THR* 4.3 18.8 + - - +
167G HIS* 3.2 26.0 + - - -
169G PHE* 3.7 8.2 - - - -
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Residues in contact with ASN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ALA* 3.7 13.7 - - - +
111F ALA 3.8 4.9 - - - +
113F THR* 5.0 5.4 + - - +
136F ASN* 1.3 79.8 - - - +
138F PHE* 1.3 58.7 + - - +
166F ASP* 5.2 3.8 + - - +
169F ASP* 3.2 15.1 + - - +
171F THR* 3.1 28.9 + - + +
172F TYR 3.0 13.5 + - - -
173F SER* 3.0 4.9 + - - -
167G HIS* 3.4 34.3 + - - -
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Residues in contact with PHE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ALA* 3.2 18.2 - - - +
112F PRO* 3.6 27.4 - - + -
135F LEU* 3.2 34.5 - - + -
136F ASN 4.1 0.2 - - - -
137F ASN* 1.3 75.8 - - - +
139F TYR* 1.3 61.5 + - - +
140F PRO 3.2 27.1 - - - -
141F LYS* 3.7 19.3 - - - -
143F ILE* 3.8 29.6 - - + -
162F TRP* 5.0 3.6 - + - -
171F THR* 3.6 1.6 - - - -
172F TYR* 2.8 52.4 + - + +
173F SER* 3.6 9.2 - - - -
174F MET* 4.0 4.7 - - + -
197F HIS* 3.6 9.0 - + + -
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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