Contacts of the strand formed by residues 129 - 139 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210E ILE* 6.1 1.6 - - - -
100H TYR* 4.1 22.0 - - + +
122H ILE* 4.4 2.0 - - + -
123H SER 3.6 4.3 - - - +
124H CYS* 2.0 44.6 - - - -
128H GLU* 1.3 77.3 - - - +
130H ARG* 1.3 64.7 + - - +
162H PRO* 4.0 3.8 - - - +
163H VAL* 3.3 41.3 + - + +
410H PHE* 4.9 0.7 - - - -
412H LEU* 4.4 13.5 - - - -
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Residues in contact with ARG 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H ILE* 3.3 6.8 - - - +
123H SER 2.9 31.1 + - - +
128H GLU* 3.4 38.6 + - + +
129H CYS* 1.3 78.0 - - - +
131H THR* 1.3 63.1 + - - +
132H PHE* 4.1 15.9 - - + -
160H SER* 3.0 47.1 + - - -
161H CYS* 3.5 14.8 - - - +
162H PRO* 4.1 14.3 - - + +
163H VAL* 3.6 2.7 - - - +
170H ASN 5.2 0.8 + - - -
172H ARG* 3.6 42.1 - - - +
174H GLU* 4.7 0.2 + - - -
189H TRP* 4.0 20.6 - - + +
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Residues in contact with THR 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H ASP* 5.4 3.8 - - - +
120H PRO* 4.6 8.1 - - + -
121H PHE 3.5 15.5 - - - +
122H ILE* 3.9 7.7 - - + +
130H ARG* 1.3 72.3 - - - +
132H PHE* 1.3 71.0 + - - +
133H PHE* 3.4 12.8 - - + -
160H SER* 3.1 4.2 - - - -
161H CYS* 2.7 43.7 + - - -
163H VAL* 3.3 28.6 - - - +
164H GLY 4.2 2.9 + - - -
165H GLU 5.6 1.1 + - - -
167H PRO* 6.4 1.6 - - + -
443H SER* 4.8 12.4 + - - +
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Residues in contact with PHE 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H PRO* 3.2 0.5 - - - +
121H PHE* 2.7 69.8 + + + -
123H SER* 4.0 9.9 - - - -
130H ARG* 4.2 17.3 - - + -
131H THR* 1.3 77.8 - - - +
133H PHE* 1.3 67.7 + - - +
158H LEU* 4.3 9.6 - - + -
159H MET 3.3 5.6 - - - -
160H SER* 3.6 13.5 - - - -
172H ARG* 6.0 0.2 - - - -
174H GLU* 3.6 35.0 - - + -
182H ALA* 4.0 18.2 - - + -
189H TRP* 3.8 48.2 - + - -
191H THR* 4.3 4.3 - - + -
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Residues in contact with PHE 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H PHE* 4.3 5.4 - + - -
117H ILE* 3.7 38.4 - - + -
119H GLU 4.1 2.2 - - - -
120H PRO* 4.0 10.3 - - + -
121H PHE* 5.5 0.2 - - - -
131H THR* 3.4 24.2 - - + -
132H PHE* 1.3 82.8 - - - +
134H LEU* 1.3 63.2 + - - +
135H THR* 3.7 14.4 - - + -
157H THR 3.5 1.7 - - - +
158H LEU* 3.5 6.4 - - - +
159H MET* 2.9 55.4 + - + -
160H SER* 3.7 4.7 - - - -
161H CYS* 3.8 10.1 - - - -
167H PRO* 3.3 30.3 - - + -
171H SER* 3.5 17.3 - - - -
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Residues in contact with LEU 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H ILE* 3.2 22.3 - - - -
118H ARG 3.2 17.2 + - - +
119H GLU* 3.8 21.1 + - + +
121H PHE* 6.4 0.4 - - + -
133H PHE* 1.3 72.1 - - - +
135H THR* 1.3 64.4 + - - +
156H ARG* 3.3 17.1 + - + +
157H THR 3.5 0.7 - - - +
158H LEU* 3.9 32.3 - - + -
177H ALA 3.8 21.1 - - - +
178H TRP* 3.6 9.2 - - - +
179H SER* 3.6 28.0 - - - +
180H ALA* 4.2 9.2 - - + +
227H GLU* 3.9 13.0 - - - +
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Residues in contact with THR 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H PHE* 4.0 20.6 - - + -
116H VAL 3.5 10.1 - - - -
117H ILE* 4.3 0.9 - - - -
133H PHE* 3.7 28.0 - - + -
134H LEU* 1.3 73.2 - - - +
136H GLN* 1.3 61.5 + - - +
137H GLY* 3.6 10.9 + - - -
156H ARG* 2.9 30.3 + - - +
157H THR* 2.6 40.4 + - - +
159H MET* 3.8 20.1 - - + -
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Residues in contact with GLN 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ARG* 2.6 31.9 + - - -
116H VAL* 3.3 36.6 + - + +
117H ILE* 5.0 1.1 - - - -
118H ARG* 5.6 1.8 - - - +
135H THR* 1.3 73.3 - - - +
137H GLY* 1.3 55.1 + - - +
138H ALA* 3.0 2.1 + - - +
148H THR* 3.2 49.2 + - + +
150H LYS* 4.6 9.3 - - - +
151H ASP* 4.5 10.7 + - - +
153H SER* 4.2 8.0 + - - -
155H HIS* 4.2 7.4 - - - +
156H ARG* 3.0 46.7 + - - +
439H THR 5.2 0.2 - - - +
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Residues in contact with GLY 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ASN* 3.8 30.7 - - - +
107F ARG* 2.8 37.0 + - - +
108F ILE* 4.3 6.1 - - - +
115H PHE* 5.4 3.1 - - - -
135H THR* 3.4 12.3 + - - -
136H GLN* 1.3 77.9 - - - +
138H ALA* 1.3 56.8 + - - +
155H HIS 3.6 6.0 + - - -
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Residues in contact with ALA 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ARG* 4.0 0.9 - - - +
108F ILE* 4.9 6.3 - - - +
115H PHE* 3.5 15.0 - - - -
116H VAL* 3.0 34.1 + - + +
136H GLN* 3.0 6.3 - - + +
137H GLY* 1.3 81.7 - - - +
139H LEU* 1.3 65.9 + - - +
144H HIS* 3.4 41.7 - - + +
145H SER* 4.1 1.6 - - - +
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Residues in contact with LEU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ARG 5.7 0.2 + - - -
108F ILE* 3.6 23.1 - - + +
111F LYS* 3.9 16.8 - - + -
112F GLY* 3.4 36.1 - - - +
113H ASP* 3.9 23.8 - - + +
114H VAL 3.4 24.7 - - - +
115H PHE* 3.8 11.2 - - + +
116H VAL* 4.2 3.6 - - - -
138H ALA* 1.3 81.1 - - - +
140H LEU* 1.3 65.0 + - - +
142H ASP* 3.4 13.7 + - + +
145H SER* 3.4 19.8 - - - -
169H PRO* 3.9 14.1 - - + -
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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