Contacts of the strand formed by residues 125 - 129 (chain H) in PDB entry 4OQT
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 SER 125 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122H LYS* 5.1 5.9 + - - +
123H GLY 3.8 0.8 + - - -
124H PRO* 1.3 74.0 + - - +
126H VAL* 1.3 60.9 + - - +
127H PHE* 3.7 28.0 - - - -
146H LEU 3.2 1.9 - - - +
147H VAL* 3.7 1.4 - - - -
148H LYS* 2.9 39.8 + - - +
149H ASP* 4.4 4.4 + - - -
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Residues in contact with VAL 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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124H PRO* 4.1 8.7 + - + +
125H SER* 1.3 78.1 - - - +
127H PHE* 1.3 74.7 + - - +
145H CYS* 4.1 17.0 - - + -
146H LEU 3.4 5.2 - - - +
147H VAL* 4.5 4.0 - - + -
201H CYS* 4.1 0.2 - - - -
203H VAL* 3.6 45.5 - - + -
212H VAL* 4.3 16.4 - - + -
214H LYS* 3.5 34.9 - - + +
124L GLU* 3.4 14.7 - - - +
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Residues in contact with PHE 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 SER* 3.7 30.5 - - - -
126H VAL* 1.3 88.2 - - - +
128H PRO* 1.4 67.9 - - - +
129H LEU* 6.4 0.2 - - + -
145H CYS* 3.4 5.1 - - - -
146H LEU* 2.6 58.6 + - + +
148H LYS* 4.3 13.5 - - + -
214H LYS* 5.4 0.9 - - - -
122L SER* 3.3 24.2 - - - +
124L GLU* 4.0 20.4 - - + -
125L GLN* 3.5 50.9 - - + +
128L SER* 5.3 7.0 - - - -
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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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127H PHE* 1.4 87.2 - - + +
129H LEU* 1.3 64.4 + - - +
130H ALA* 3.4 14.9 + - + +
144H GLY 3.8 5.4 - - - +
145H CYS* 5.1 0.9 - - - -
214H LYS* 4.6 6.5 - - + -
215H LYS 4.2 19.3 - - - +
216H VAL* 4.4 12.8 - - + -
217H GLU 5.3 1.1 - - - +
120L PRO 4.9 6.4 - - - +
122L SER* 3.8 24.2 + - - -
124L GLU* 3.8 19.7 - - + +
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Residues in contact with LEU 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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127H PHE 3.7 0.2 + - - -
128H PRO* 1.3 72.6 - - - +
130H ALA* 1.3 66.7 + - - +
131H PRO 3.4 0.2 - - - -
143H LEU* 3.3 7.4 - - - -
144H GLY 2.7 47.3 + - - +
145H CYS 4.1 8.3 - - - +
146H LEU* 4.4 10.5 - - + +
184H SER* 3.5 28.9 - - - +
186H VAL* 4.2 15.7 - - + -
216H VAL* 3.4 3.5 - - - +
119L PHE* 3.5 38.4 - - + +
120L PRO 4.9 5.8 - - - +
121L PRO* 6.3 0.4 - - + -
132L SER 5.9 1.8 - - - +
134L VAL* 4.0 22.9 - - + +
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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