Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 2FE4
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 ILE 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A THR 3.5 10.6 + - - +
88A VAL* 3.5 13.0 - - + +
89A ALA 3.0 24.9 + - - +
119A VAL* 1.3 81.0 - - - +
121A ILE* 1.3 65.6 + - - +
151A MET* 4.2 16.6 - - + -
170A VAL* 4.6 2.9 - - + +
173A ALA* 3.4 52.5 - - + +
174A LEU* 3.7 23.6 - - + +
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Residues in contact with ILE 121 (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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89A ALA* 3.5 10.3 - - + +
91A VAL* 4.3 19.7 - - + -
108A ILE* 4.4 13.5 - - + -
111A VAL* 4.1 24.9 - - + -
112A ARG* 4.1 24.9 - - + +
119A VAL* 4.1 18.3 + - + +
120A ILE* 1.3 81.9 - - - +
122A MET* 1.3 66.0 + - - +
123A LEU 4.7 0.4 - - - +
150A VAL* 3.4 34.4 - - + +
151A MET* 2.8 30.2 + - - +
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Residues in contact with MET 122 (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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88A VAL* 5.3 1.3 - - + +
89A ALA 3.0 10.7 + - - +
90A VAL* 3.5 5.4 - - + -
91A VAL 2.9 25.3 + - - -
120A ILE* 4.3 0.6 - - + -
121A ILE* 1.3 76.1 - - - +
123A LEU* 1.3 60.5 + - - +
124A VAL* 3.7 6.3 + - + +
151A MET* 3.7 13.0 - - + -
152A PHE 3.6 22.9 - - - -
153A ILE* 3.5 24.5 - - + -
166A LEU* 3.4 28.9 - - + +
169A ARG* 3.9 39.0 - - + +
170A VAL* 3.7 26.9 - - + -
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Residues in contact with LEU 123 (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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91A VAL* 3.5 20.6 - - + +
93A TYR* 4.0 13.7 - - + -
101A PHE* 4.8 3.6 - - + -
104A THR* 4.0 32.3 - - + +
108A ILE* 4.7 8.5 - - + -
121A ILE* 4.1 1.0 - - - -
122A MET* 1.3 72.9 - - - +
124A VAL* 1.3 61.2 + - - +
141A GLY 3.9 12.3 - - - +
144A ARG* 4.4 13.5 - - + -
145A ALA* 4.0 14.6 - - + +
150A VAL* 4.1 10.9 - - + +
151A MET 2.7 18.5 + - - +
152A PHE* 3.3 25.1 - - + -
153A ILE 3.1 24.1 + - - +
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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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29A LEU* 4.5 12.8 - - + -
90A VAL* 3.6 28.7 - - + -
91A VAL 2.8 13.0 + - - +
92A VAL* 3.5 8.0 - - + -
93A TYR* 2.9 35.6 + - - +
122A MET* 3.7 14.4 - - + +
123A LEU* 1.3 80.3 - - - +
125A GLY* 1.3 61.0 + - - +
126A ASN 4.3 0.9 - - - +
153A ILE* 3.2 10.3 - - + +
155A THR* 3.4 33.7 - - + +
166A LEU* 3.8 10.5 - - + -
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Residues in contact with GLY 125 (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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93A TYR* 3.5 33.5 + - - -
95A ILE* 3.9 7.0 - - - -
124A VAL* 1.3 68.6 - - - +
126A ASN* 1.3 57.7 + - - -
128A THR* 3.8 2.6 - - - +
152A PHE* 4.3 2.0 - - - -
153A ILE 3.0 11.9 + - - -
154A GLU* 3.1 13.6 - - - +
155A THR 2.8 29.3 + - - +
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Residues in contact with ASN 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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24A VAL 2.7 25.0 + - - +
25A GLY* 3.7 7.5 + - - -
29A LEU* 3.8 10.2 - - + +
92A VAL* 3.9 11.0 - - + -
93A TYR 3.0 17.7 + - - +
94A ASP* 3.8 0.5 - - - -
95A ILE* 3.2 23.1 + - - +
124A VAL* 3.4 1.0 + - + -
125A GLY* 1.3 73.1 - - - +
127A LYS* 1.3 88.2 + - - +
128A THR 3.4 1.1 - - - -
155A THR* 3.0 22.2 + - - +
156A SER* 3.5 0.5 - - - -
157A ALA 3.4 10.6 + - - -
201A GDP 3.2 33.2 + - - +
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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