Contacts of the strand formed by residues 125 - 131 (chain H) in PDB entry 2Q5E
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 125 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269B ARG 6.5 0.7 - - - -
113H VAL* 4.8 1.1 - - + -
123H ALA* 4.2 2.1 - - - +
124H ASP* 1.3 89.0 - - + +
126H ILE* 1.3 67.7 + - - +
127H VAL* 4.2 4.3 - - + -
139H TYR* 3.6 0.2 - - - -
140H VAL* 2.7 64.4 + - + +
142H LYS* 3.4 39.9 - - + -
173H VAL* 4.5 6.1 - - + -
176H LEU* 3.8 57.7 - - + -
177H LEU* 3.9 20.4 - - + -
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Residues in contact with ILE 126 (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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269B ARG* 5.1 33.6 - - + +
120H ILE 5.3 2.7 - - - +
123H ALA* 4.6 11.4 - - + +
125H PHE* 1.3 79.1 - - - +
127H VAL* 1.3 68.5 + - - +
128H PRO* 4.3 3.8 - - + +
137H GLN* 3.7 39.7 - - + +
138H VAL 3.2 6.7 - - - +
139H TYR* 3.5 33.4 - - + -
176H LEU* 4.8 4.5 - - - +
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Residues in contact with VAL 127 (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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125H PHE* 4.2 8.3 - - + -
126H ILE* 1.3 81.9 - - - +
128H PRO* 1.3 65.8 - - + +
129H ILE* 3.8 24.0 + - + -
137H GLN* 4.2 2.5 - - - -
138H VAL* 2.7 43.5 + - + +
140H VAL* 4.6 3.4 - - + -
172H PRO* 4.0 26.7 - - + +
173H VAL* 4.3 22.2 - - + -
176H LEU* 4.0 23.1 - - + -
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Residues in contact with PRO 128 (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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227B PRO* 6.2 0.4 - - + -
126H ILE* 4.3 3.8 - - + +
127H VAL* 1.3 86.6 - - + +
129H ILE* 1.3 63.4 - - - +
130H GLU 4.5 0.2 + - - -
135H THR* 4.2 13.2 - - - +
136H HIS 3.4 1.8 - - - +
137H GLN* 3.2 25.8 - - - +
172H PRO* 5.4 4.2 - - - +
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Residues in contact with ILE 129 (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 PHE* 4.7 8.7 - - + -
127H VAL* 3.9 16.8 - - + -
128H PRO* 1.3 79.1 - - - +
130H GLU* 1.3 64.5 + - - +
131H ILE* 3.7 24.6 + - + +
134H THR 3.6 1.2 - - - +
135H THR* 3.2 3.0 - - - -
136H HIS* 2.7 39.4 + - - +
138H VAL* 3.3 28.5 - - + -
168H LYS* 4.2 26.2 - - + +
169H TYR* 3.8 33.2 - - + -
172H PRO* 5.2 0.7 - - + -
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Residues in contact with GLU 130 (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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130D GLU* 5.1 16.3 - - + +
168D LYS* 4.8 17.5 - - - +
128H PRO 4.3 0.2 - - - -
129H ILE* 1.3 74.1 - - - +
131H ILE* 1.3 60.7 + - - +
132H GLU* 3.4 6.4 + - - -
133H GLY* 2.7 46.3 + - - +
134H THR 3.6 3.8 - - - -
135H THR* 3.8 17.7 - - + +
168H LYS* 3.9 19.0 + - + +
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Residues in contact with ILE 131 (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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194C PHE* 4.8 20.9 - - + -
199C TYR* 5.6 4.0 - - - +
117H PHE* 4.8 14.6 - - + -
129H ILE* 4.1 19.1 - - + +
130H GLU* 1.3 76.4 - - - +
132H GLU* 1.3 89.3 + - + +
133H GLY 2.8 1.3 + - - -
134H THR* 2.8 28.4 + - - +
136H HIS* 4.0 16.2 - - + +
168H LYS* 3.2 35.7 - - - +
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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