Contacts of the strand formed by residues 123 - 128 (chain A) in PDB entry 3F2F
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 PRO 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A SER 3.5 9.0 - - - +
116A HIS* 3.6 15.7 - - + +
121A GLY 3.5 4.0 - - - +
122A ALA* 1.3 90.1 - - + +
124A VAL* 1.3 62.9 + - - +
137A GLU 4.3 1.0 - - - +
138A PRO* 4.1 9.5 - - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 3.3 2.3 - - - -
115A SER* 2.9 59.9 + - - +
116A HIS* 3.9 2.9 - - - +
117A CYS* 4.2 6.5 - - + +
122A ALA 3.8 8.1 - - - +
123A PRO* 1.3 81.8 - - - +
125A SER* 1.3 64.2 + - - +
126A LEU* 6.2 0.4 - - + -
137A GLU 3.3 4.7 - - - -
138A PRO* 3.8 15.7 - - + -
141A MET* 3.7 13.0 - - + -
164A PHE* 3.9 21.1 - - + -
165A PHE 4.4 4.9 - - - +
166A ALA* 4.4 19.3 - - + +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 5.8 3.2 + - - -
113A VAL 3.2 15.5 - - - -
114A SER* 4.0 9.9 - - - +
124A VAL* 1.3 78.1 - - - +
126A LEU* 1.3 70.4 + - - +
135A ALA 3.4 2.6 + - - +
137A GLU* 2.8 48.0 + - - +
141A MET* 3.4 3.1 - - - +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 4.0 6.3 - - + -
112A ARG* 3.9 2.4 - - - -
113A VAL* 2.9 56.4 + - + +
124A VAL* 6.2 0.4 - - + -
125A SER* 1.3 82.0 - - - +
127A THR* 1.3 63.8 + - - +
128A VAL* 3.7 21.8 - - + -
133A ILE* 4.1 17.5 - - + -
134A GLN 3.7 8.5 - - - +
135A ALA 3.4 9.2 - - - -
136A VAL* 3.9 11.2 - - + -
141A MET* 4.1 20.6 - - + -
164A PHE* 4.3 9.6 - - + -
189A VAL* 3.9 23.8 - - + -
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 3.3 31.6 - - + -
111A ALA 3.5 8.1 - - - +
112A ARG* 3.8 29.5 + - + +
126A LEU* 1.3 73.1 - - - +
128A VAL* 1.3 60.8 + - - +
129A SER* 4.1 0.9 - - - +
132A GLU 4.1 0.5 - - - +
133A ILE* 3.3 6.1 - - - +
134A GLN* 2.8 51.2 + - + -
135A ALA* 4.1 10.7 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A THR 3.8 9.9 - - - +
101A LEU* 3.9 21.3 - - + +
104A PRO* 3.5 29.0 - - + +
110A THR* 3.4 3.3 - - - -
111A ALA 2.9 34.1 + - - +
113A VAL* 3.7 23.6 - - + -
126A LEU* 3.7 25.4 - - + -
127A THR* 1.3 76.5 - - - +
129A SER* 1.3 67.7 + - - +
132A GLU 3.9 1.6 - - - -
133A ILE* 4.2 3.8 - - + -
193A PHE* 3.9 11.4 - - + -
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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