Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 1F5F
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 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A MET* 3.4 8.8 - - - +
108A GLU* 2.9 34.9 + - - -
109A GLY 3.3 0.8 - - - +
110A ASP* 1.3 92.5 + - - +
112A VAL* 1.3 64.1 + - - +
113A LEU* 3.8 17.3 - - - -
123A ARG* 4.0 11.5 + - - +
124A LEU 3.0 10.8 - - - -
125A ARG* 3.5 20.8 + - - +
127A VAL* 4.2 0.2 - - - -
128A SER* 5.4 0.2 - - - -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 4.1 14.8 - - + -
78A ILE* 4.9 7.4 - - + +
80A LEU* 4.6 7.2 - - + -
105A VAL* 3.9 26.5 - - + -
106A LYS 3.4 4.5 - - - +
107A MET* 3.7 21.5 - - + -
111A SER* 1.3 75.8 - - - +
113A LEU* 1.3 64.5 + - - +
114A LEU 4.2 0.2 + - - -
122A LEU* 4.1 0.9 - - - +
123A ARG* 3.5 1.4 - - - -
124A LEU* 2.8 47.3 + - + +
127A VAL* 3.7 20.9 - - + -
128A SER* 5.0 1.1 - - - -
253A DHT 4.3 17.7 - - + -
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU 3.7 0.5 - - - +
105A VAL* 3.3 8.5 - - - +
106A LYS* 2.8 56.0 + - + +
108A GLU* 4.0 22.9 - - + -
111A SER* 3.8 11.4 - - - -
112A VAL* 1.3 80.2 - - - +
114A LEU* 1.3 62.3 + - - +
115A GLU* 4.2 9.2 - - + +
120A GLU* 4.1 9.2 - - + +
122A LEU 3.5 4.5 - - - +
123A ARG* 3.1 62.1 - - + +
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Residues in contact with LEU 114 (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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69A LEU* 4.3 13.7 - - + -
76A PRO* 3.8 28.5 - - + -
78A ILE* 4.4 13.7 - - + -
91A ALA* 5.0 1.6 - - + +
103A VAL* 3.8 18.4 - - + -
104A GLU 3.5 14.1 - - - +
105A VAL* 3.7 17.7 - - + -
113A LEU* 1.3 74.7 - - - +
115A GLU* 1.4 64.7 + - - +
116A VAL* 4.5 1.6 - - + -
120A GLU* 3.6 3.1 - - - +
121A VAL* 2.8 45.6 + - + -
122A LEU* 2.8 35.5 + - + +
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Residues in contact with GLU 115 (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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103A VAL* 3.3 8.5 - - - +
104A GLU* 2.6 70.5 + - + +
106A LYS* 4.5 12.0 - - + +
113A LEU* 5.2 10.6 - - + +
114A LEU* 1.4 78.7 - - - +
116A VAL* 1.3 65.0 + - - +
117A ASP 4.3 0.2 - - - -
118A GLY* 4.5 12.3 - - - +
119A GLU 3.2 12.1 - - - +
120A GLU* 4.0 20.3 + - + +
254A IPA 2.9 25.9 - - - +
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Residues in contact with VAL 116 (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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76A PRO* 4.5 17.9 - - + -
93A PRO* 4.2 14.6 - - + -
95A LEU* 4.0 24.9 - - + -
101A HIS* 4.9 2.0 - - + -
102A GLN 3.4 7.9 - - - +
103A VAL* 4.8 9.9 - - + -
114A LEU* 4.3 5.8 + - + -
115A GLU* 1.3 78.5 - - - +
117A ASP* 1.3 75.3 + - + +
118A GLY 3.1 1.1 - - - -
119A GLU* 2.7 43.0 + - + +
121A VAL* 3.9 29.1 - - + +
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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
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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