Contacts of the strand formed by residues 129 - 139 (chain F) in PDB entry 2HU4
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 CYS 129 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100F TYR* 4.1 22.0 - - + +
122F ILE* 4.5 1.8 - - + -
124F CYS* 2.1 47.8 - - - -
128F GLU* 1.3 78.2 - - - +
130F ARG* 1.3 63.2 + - - +
162F PRO* 4.2 4.2 - - - +
163F VAL* 3.2 41.2 + - + +
410F PHE* 5.0 0.2 - - - -
412F LEU* 4.1 17.0 - - - -
210H ILE* 5.7 2.5 - - - -
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Residues in contact with ARG 130 (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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122F ILE* 3.4 4.7 - - - +
123F SER 3.0 32.6 + - - +
128F GLU* 3.4 36.9 + - + +
129F CYS* 1.3 78.2 - - - +
131F THR* 1.3 64.4 + - - +
132F PHE* 4.0 17.5 - - + -
160F SER* 3.1 46.2 + - - -
161F CYS* 3.4 14.9 - - - +
162F PRO* 4.5 12.9 - - + +
163F VAL* 3.9 2.9 - - - +
170F ASN 5.1 1.4 + - - -
172F ARG* 3.4 42.0 - - - +
189F TRP* 4.0 18.8 - - + +
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Residues in contact with THR 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ASP* 5.4 2.7 - - - +
120F PRO* 4.8 6.1 - - + -
121F PHE 3.5 10.5 - - - +
122F ILE* 3.6 11.5 - - + +
130F ARG* 1.3 72.9 - - - +
132F PHE* 1.3 70.1 + - - +
133F PHE* 3.5 13.2 - - + -
160F SER* 3.3 4.0 - - - -
161F CYS* 2.9 40.2 + - - -
162F PRO 4.7 0.2 - - - -
163F VAL* 3.2 29.5 - - - +
164F GLY 4.2 2.8 + - - -
165F GLU 5.8 1.6 - - - +
167F PRO* 6.5 1.1 - - + -
443F SER* 4.7 14.8 + - - +
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Residues in contact with PHE 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F PRO* 3.4 1.0 - - - +
121F PHE* 2.7 71.5 + + + -
123F SER* 4.0 9.6 - - - -
130F ARG* 4.0 17.5 - - + -
131F THR* 1.3 78.3 - - - +
133F PHE* 1.3 67.4 + - - +
158F LEU* 4.3 7.9 - - + -
159F MET 3.4 5.8 - - - -
160F SER* 3.7 13.7 - - - -
174F GLU* 3.7 33.4 - - + -
182F ALA* 3.9 17.7 - - + -
189F TRP* 3.6 48.7 - + - -
191F THR* 4.3 4.3 - - + -
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Residues in contact with PHE 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F PHE* 4.2 5.6 - + - -
117F ILE* 3.7 37.9 - - + -
118F ARG 4.4 0.2 - - - +
119F GLU 3.9 8.3 - - - -
120F PRO* 4.2 5.8 - - + -
121F PHE* 5.3 0.4 - - - -
131F THR* 3.5 24.9 - - + -
132F PHE* 1.3 83.6 - - - +
134F LEU* 1.3 63.9 + - - +
135F THR* 3.9 15.0 - - + -
157F THR 3.5 0.5 - - - +
158F LEU* 3.3 6.0 - - - +
159F MET* 2.8 57.0 + - + -
160F SER* 3.7 5.4 - - - -
161F CYS* 3.7 9.9 - - - -
167F PRO* 3.3 30.1 - - + -
171F SER* 3.6 16.6 - - - -
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F ILE* 3.4 3.8 - - - -
118F ARG 3.2 32.1 + - - +
119F GLU* 3.7 35.2 - - + +
121F PHE* 6.2 1.3 - - + -
133F PHE* 1.3 73.6 - - - +
135F THR* 1.3 65.5 + - - +
156F ARG* 3.8 13.7 + - + +
157F THR 3.2 2.2 - - - +
158F LEU* 3.9 31.4 - - + -
177F ALA 3.6 19.7 - - - +
178F TRP* 3.6 28.5 - - - +
179F SER* 3.7 7.4 - - - +
180F ALA* 4.1 11.0 - - + +
227F GLU* 4.0 5.8 - - - +
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Residues in contact with THR 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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115F PHE* 3.8 37.8 - - + -
116F VAL 3.5 10.1 - - - -
117F ILE* 4.1 0.7 - - - -
133F PHE* 3.9 18.6 - - + -
134F LEU* 1.3 72.7 - - - +
136F GLN* 1.3 59.1 + - - +
137F GLY* 3.2 14.1 + - - -
156F ARG* 2.7 35.0 + - - +
157F THR* 2.5 42.3 + - - +
159F MET* 3.9 8.5 - - + -
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Residues in contact with GLN 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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116F VAL* 3.3 34.9 + - + +
117F ILE* 4.9 1.6 - - - -
118F ARG* 5.3 2.8 - - - +
135F THR* 1.3 75.3 - - - +
137F GLY* 1.3 55.1 + - - +
138F ALA* 3.2 0.9 + - - +
148F THR* 3.3 48.6 + - + +
150F LYS* 4.7 10.9 - - - +
151F ASP 4.7 7.7 - - - +
153F SER* 4.5 5.9 + - - -
155F HIS* 4.2 8.5 - - - +
156F ARG* 2.9 54.0 - - - +
439F THR 5.2 0.2 - - - +
107G ARG* 2.4 34.3 + - - -
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Residues in contact with GLY 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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115F PHE* 5.2 2.7 - - - -
135F THR* 3.2 14.1 + - - -
136F GLN* 1.3 79.2 - - - +
138F ALA* 1.3 56.9 + - - +
155F HIS 3.9 1.8 + - - -
104G ASN* 3.4 29.7 - - - +
107G ARG* 2.9 35.8 + - - +
108G ILE* 4.4 8.7 - - - -
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Residues in contact with ALA 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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115F PHE* 3.4 14.2 - - - -
116F VAL* 3.1 34.8 + - + +
136F GLN* 3.2 5.5 - - + +
137F GLY* 1.3 81.7 - - - +
139F LEU* 1.3 66.6 + - - +
144F HIS* 3.5 41.5 - - + +
145F SER* 4.1 1.8 - - - +
107G ARG* 4.1 3.4 - - - +
108G ILE* 4.8 4.3 - - - -
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Residues in contact with LEU 139 (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 ASP* 3.7 24.2 - - + +
114F VAL 3.3 17.7 - - - +
115F PHE* 3.7 24.0 - - + +
116F VAL* 4.6 2.5 - - - -
138F ALA* 1.3 85.8 - - - +
140F LEU* 1.3 71.5 + - - +
142F ASP* 3.4 20.4 + - + +
145F SER* 3.6 11.0 - - - -
169F PRO* 4.1 11.0 - - + -
107G ARG 5.3 1.2 + - - -
108G ILE* 4.0 18.4 - - + +
111G LYS* 4.1 12.8 - - + -
112G GLY* 3.5 36.3 - - - +
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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