Contacts of the strand formed by residues 115 - 124 (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 PHE 115 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108F ILE* 3.6 30.7 - - + -
114H VAL* 1.3 84.0 - - - +
116H VAL* 1.3 62.7 + - - +
117H ILE* 3.6 22.8 + - + +
133H PHE* 4.3 6.3 - + - -
135H THR* 4.0 22.0 - - + -
137H GLY* 5.4 1.6 - - - -
138H ALA 3.5 19.5 - - - -
139H LEU* 3.8 5.5 - - + +
140H LEU* 4.2 3.3 - - - +
159H MET* 3.8 31.9 - - + -
167H PRO* 2.8 20.2 + - + +
168H SER 3.6 17.5 - - - -
169H PRO* 3.4 37.2 - - + -
171H SER* 4.2 1.3 - - - -
440H SER* 4.2 3.1 + - - -
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Residues in contact with VAL 116 (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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114H VAL 3.7 2.0 + - - -
115H PHE* 1.3 73.2 - - - +
117H ILE* 1.3 65.5 + - - +
135H THR* 3.5 1.9 - - - -
136H GLN* 3.3 42.6 + - + -
138H ALA* 3.0 39.6 + - + +
139H LEU 3.9 5.4 - - - +
140H LEU* 3.8 15.9 - - + -
145H SER* 4.8 5.4 - - - +
148H THR* 3.8 11.7 - - + +
438H TRP* 5.8 0.4 - - + -
439H THR 3.2 25.8 - - - +
440H SER* 3.5 7.9 - - - -
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Residues in contact with ILE 117 (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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103H ASP* 5.8 2.9 - - - +
105H SER* 5.4 0.4 - - - +
115H PHE* 3.6 20.0 - - + +
116H VAL* 1.3 83.9 - - - +
118H ARG* 1.3 66.5 + - - +
120H PRO* 3.9 20.2 - - + -
131H THR* 6.3 0.2 - - + -
133H PHE* 3.7 41.5 - - + -
134H LEU 3.2 15.5 - - - +
135H THR* 4.3 1.6 - - - +
136H GLN* 5.3 0.6 - - - +
156H ARG* 4.3 2.7 - - - +
167H PRO* 4.4 15.7 - - + -
439H THR 4.0 1.6 - - - +
440H SER* 2.9 33.5 + - - +
441H GLY 3.3 28.5 + - - +
442H SER* 5.7 0.9 - - - -
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Residues in contact with ARG 118 (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* 1.3 85.2 - - - +
119H GLU* 1.3 108.2 + - - +
120H PRO* 3.3 5.2 - - - +
134H LEU 3.2 20.4 + - - +
136H GLN* 5.6 1.1 - - - +
148H THR 5.3 3.4 - - - +
151H ASP* 5.2 2.0 + - - -
156H ARG* 3.4 9.4 - - - +
371H ARG* 4.7 0.8 - - - +
406H TYR* 3.5 28.1 - - - -
425H GLU* 2.4 41.9 + - - -
427H ILE* 3.7 22.0 - - - +
439H THR* 4.1 30.7 - - + +
440H SER* 4.3 7.6 - - - -
441H GLY* 5.0 1.1 - - - +
807H G39 3.8 18.2 + - - +
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Residues in contact with GLU 119 (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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118H ARG* 1.3 115.5 + - - +
120H PRO* 1.3 72.5 - - - +
121H PHE* 3.8 14.3 - - - -
133H PHE* 4.1 6.1 - - - -
134H LEU* 3.8 18.5 + - + +
151H ASP* 4.5 0.5 - - - +
156H ARG* 3.2 22.7 + - - -
227H GLU* 4.0 32.6 - - + +
406H TYR* 4.4 17.0 - - + -
425H GLU* 3.0 10.4 + - - -
807H G39 3.1 28.9 + - - +
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Residues in contact with PRO 120 (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* 3.9 23.3 - - + -
118H ARG* 3.3 5.1 - - - -
119H GLU* 1.3 92.6 - - - +
121H PHE* 1.3 65.9 + - - +
131H THR* 4.6 9.2 - - + -
132H PHE 3.2 13.0 - - - +
133H PHE* 4.0 3.6 - - + -
423H TRP* 3.3 19.9 - - + -
425H GLU* 3.4 36.1 - - + +
441H GLY* 5.7 1.1 - - - +
442H SER 4.5 8.3 - - - +
443H SER* 4.6 10.8 - - - -
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Residues in contact with PHE 121 (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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119H GLU 3.8 11.7 - - - -
120H PRO* 1.3 76.1 - - - +
122H ILE* 1.3 69.3 + - - +
123H SER* 4.5 0.9 - - - -
131H THR* 3.5 3.6 - - - +
132H PHE* 2.7 75.7 + + + -
134H LEU* 6.4 0.4 - - + -
158H LEU* 4.6 10.3 - - + -
180H ALA* 4.7 2.2 - - + -
181H SER* 4.0 13.9 - - - -
182H ALA* 3.8 25.4 - - + -
227H GLU* 3.5 19.1 - - - +
228H SER* 3.6 10.5 - - - -
229H GLU* 3.5 28.9 - - + -
423H TRP* 3.5 27.1 - - + +
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Residues in contact with ILE 122 (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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100H TYR* 5.4 0.4 - - + -
101H SER* 4.4 4.7 - - - +
121H PHE* 1.3 80.3 - - - +
123H SER* 1.3 72.5 + - - +
129H CYS* 4.4 4.5 - - + -
130H ARG 3.3 11.0 - - - +
131H THR* 3.9 11.9 - - + +
163H VAL* 3.5 28.5 - - + -
229H GLU* 3.8 10.0 - - - +
409H SER 4.5 0.9 - - - +
410H PHE* 3.3 51.9 - - + +
423H TRP* 3.6 16.6 + - + -
443H SER* 5.8 4.9 - - - +
445H SER* 3.6 34.1 - - - +
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Residues in contact with SER 123 (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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121H PHE* 4.5 1.3 - - - -
122H ILE* 1.3 80.1 - - - +
124H CYS* 1.3 66.0 + - - +
130H ARG* 2.9 27.3 + - - +
132H PHE* 4.0 12.3 - - - -
182H ALA 3.7 7.2 + - - -
183H CYS* 3.8 4.9 - - - -
189H TRP* 3.5 30.9 - - - -
229H GLU* 2.9 32.5 + - - +
410H PHE* 4.9 1.3 - - - -
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Residues in contact with CYS 124 (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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85H LEU* 5.4 3.1 - - - +
122H ILE* 4.5 0.2 - - - -
123H SER* 1.3 80.4 + - - +
125H SER* 1.3 61.4 + - - +
128H GLU 3.2 6.3 - - - +
129H CYS* 2.0 47.1 - - - -
184H HIS* 3.7 13.5 + - - +
189H TRP* 3.9 5.6 - - - -
229H GLU* 4.2 4.1 + - - +
410H PHE* 4.1 16.8 - - - -
411H VAL 3.6 22.7 + - - +
412H HIS* 3.9 20.0 - - - +
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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