Contacts of the strand formed by residues 111 - 116 (chain B) 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 ALA 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PHE* 3.5 34.1 - - + -
86B GLU 3.3 5.4 - - - +
87B ILE* 3.4 20.0 - - + -
104B PRO* 4.2 8.3 - - + -
109B ARG 3.9 0.2 + - - -
110B THR* 1.3 73.7 - - - +
112B ARG* 1.3 64.2 + - - +
113B VAL* 3.9 4.4 + - + +
127B THR* 3.3 4.0 - - - +
128B VAL* 2.8 36.5 + - + +
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL 3.7 2.1 - - - +
85B PHE* 3.8 0.2 - - - -
86B GLU* 2.9 52.9 + - + +
110B THR* 5.1 3.8 - - - +
111B ALA* 1.3 73.3 - - - +
113B VAL* 1.3 61.4 + - - +
114B SER* 5.0 1.7 + - - +
126B LEU 3.6 4.9 + - - +
127B THR* 2.9 36.4 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 5.5 0.4 - - + -
84B VAL 3.3 9.2 - - - +
85B PHE* 4.1 15.0 - - + -
100B THR* 3.7 41.7 - - + +
111B ALA* 4.4 3.6 - - + +
112B ARG* 1.3 75.7 - - - +
114B SER* 1.3 70.9 + - - +
115B SER* 5.5 0.2 - - - -
125B SER* 3.2 8.0 - - - -
126B LEU* 2.7 55.2 + - + +
128B VAL* 4.1 21.5 - - + -
164B PHE* 4.1 8.7 - - + -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B SER 3.6 0.3 - - - +
83B TYR* 3.7 1.2 - - - -
84B VAL* 2.8 50.7 + - - +
86B GLU* 4.5 10.6 + - - -
112B ARG* 4.2 2.1 + - - +
113B VAL* 1.3 79.1 + - - +
115B SER* 1.3 63.3 + - - +
124B VAL 3.5 8.3 - - - -
125B SER* 4.4 6.3 - - - +
126B LEU* 6.0 0.2 - - - -
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 2.8 25.6 + - - -
83B TYR* 3.6 25.9 - - - -
113B VAL* 5.5 0.2 - - - -
114B SER* 1.3 77.8 - - - +
116B HIS* 1.3 88.4 + - - +
123B PRO* 3.7 1.6 - - - +
124B VAL* 2.9 38.8 + - - +
164B PHE* 4.0 9.4 - - - -
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Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B SER* 5.3 5.1 + - - -
115B SER* 1.3 96.5 + - - +
117B CYS* 1.3 68.9 + - - +
118B ALA* 3.3 4.7 + - - +
121B GLY* 3.6 23.6 - - - +
122B ALA 3.3 6.3 - - - +
123B PRO* 3.9 16.7 - - + +
124B VAL* 3.9 6.0 - - - +
163B HIS* 5.8 0.3 - - - +
164B PHE* 3.7 7.1 + - - +
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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
------------------------------------------------------------
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