Contacts of the strand formed by residues 125 - 130 (chain F) in PDB entry 3QS7
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 VAL 125 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F GLN* 5.7 4.7 - - + -
93F VAL 3.4 7.0 - - - +
94F LEU* 3.8 18.6 - - + -
116F PRO* 3.3 1.8 - - - +
117F HIS* 2.9 45.3 + - + +
118F PHE 4.7 1.2 - - - -
124F GLY* 1.3 73.5 - - - -
126F VAL* 1.4 60.4 + - - +
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Residues in contact with VAL 126 (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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92F GLN* 3.2 4.2 - - - +
93F VAL* 2.9 35.9 + - + +
103F CYS* 4.6 12.3 - - + -
105F TRP* 5.3 1.1 - - - +
116F PRO* 3.6 20.6 - - + -
124F GLY 4.3 0.2 - - - -
125F VAL* 1.4 73.1 - - - +
127F SER* 1.4 61.0 + - - +
143F LEU* 3.8 28.3 - - + -
145F ILE* 4.9 5.6 - - + -
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Residues in contact with SER 127 (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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90F THR* 5.9 4.0 - - - -
91F LEU 3.3 7.9 - - - -
92F GLN* 3.7 18.6 - - - -
105F TRP* 3.5 18.1 + - - +
114F CYS* 5.5 1.7 - - - +
116F PRO* 4.8 3.8 - - - +
126F VAL* 1.4 77.7 - - - +
128F MET* 1.4 59.9 + - - +
129F VAL* 4.2 2.2 - - - -
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Residues in contact with MET 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F LEU* 2.9 42.5 + - + +
105F TRP* 3.3 38.8 - - + +
127F SER* 1.4 69.4 - - - +
129F VAL* 1.3 59.5 + - - +
130F ILE* 5.5 1.3 - - + -
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Residues in contact with VAL 129 (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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89F ILE 4.3 0.7 - - - +
90F THR* 3.8 28.0 - - - +
127F SER* 4.2 3.4 - - - -
128F MET* 1.3 73.9 - - - +
130F ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 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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83F VAL* 5.7 4.0 - - + -
87F ALA 3.9 5.6 - - - +
88F SER* 3.2 2.9 - - - -
89F ILE* 2.9 62.5 + - + +
91F LEU* 3.8 17.0 - - + -
128F MET* 5.5 1.8 - - + +
129F VAL* 1.3 79.8 - - - +
131F LEU* 1.3 60.0 + - - +
133F MET* 3.8 29.8 - - + -
137F GLN* 5.2 14.8 - - + +
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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