Contacts of the strand formed by residues 142 - 146 (chain A) in PDB entry 3FEG
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 GLY 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG 3.1 13.5 - - - -
105A LEU* 4.3 0.4 - - - -
106A TYR* 3.5 21.3 + - - -
138A VAL* 3.9 0.3 - - - -
139A PHE* 2.9 41.5 + - - +
140A PRO 3.4 0.4 - - - -
141A GLU* 1.3 81.5 - - - +
143A ARG* 1.3 61.6 + - - +
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Residues in contact with ARG 143 (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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102A LEU 3.7 0.2 - - - +
103A LEU* 3.6 5.0 - - - +
104A ARG* 2.9 64.6 + - + +
106A TYR* 4.2 13.8 + - + +
119A GLU* 3.4 32.5 + - - +
120A SER* 5.5 2.6 - - - +
123A PHE* 3.3 36.2 - - - +
135A LEU* 4.0 20.2 - - + -
137A GLY 3.1 15.0 - - - +
138A VAL* 4.3 4.7 - - + -
139A PHE* 3.7 8.2 - - - -
142A GLY* 1.3 76.2 - - - +
144A LEU* 1.3 60.2 + - - +
145A GLU* 2.6 35.2 + - + +
265A PHE 6.2 0.2 - - - +
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Residues in contact with LEU 144 (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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52A TRP* 3.7 32.1 - - + +
53A CYS* 4.3 10.1 - - - +
56A TYR* 3.9 17.3 - - + -
57A LEU* 4.0 15.3 - - + -
101A VAL* 4.0 22.2 - - + -
102A LEU 3.4 1.1 - - - +
103A LEU* 3.9 32.5 - - + -
135A LEU* 3.7 6.4 - - - +
136A TYR* 2.8 36.8 + - + -
137A GLY 2.9 16.5 + - - +
139A PHE* 4.1 12.6 - - + -
143A ARG* 1.3 74.4 - - - +
145A GLU* 1.3 57.8 + - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 6.0 0.2 - - - -
101A VAL* 3.2 6.9 - - - +
102A LEU* 2.7 43.9 + - + +
104A ARG* 2.8 34.4 + - + -
123A PHE* 3.5 22.0 - - + -
133A PRO* 4.3 2.1 - - + +
134A GLN 3.3 10.3 - - - +
136A TYR* 3.9 6.1 - - - -
143A ARG* 2.6 41.0 + - + +
144A LEU* 1.3 76.7 - - - +
146A GLN* 1.3 64.5 + - - +
397A ADP 3.6 1.9 + - - -
398A AMP 3.3 20.2 + - - +
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Residues in contact with GLN 146 (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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98A PRO* 6.1 1.1 - - + -
100A GLU 4.1 4.7 - - - +
102A LEU* 4.4 0.6 - - - +
132A GLY 4.7 0.5 - - - +
133A PRO* 3.7 3.6 - - - +
134A GLN* 2.8 50.9 + - - +
136A TYR* 3.6 24.2 - - + +
145A GLU* 1.3 73.1 - - - +
147A TYR* 1.3 68.6 + - - +
148A ILE* 3.2 27.6 + - + +
149A PRO* 5.2 4.0 - - - +
261A MET* 5.2 2.5 - - - +
397A ADP 2.9 1.7 + - - -
398A AMP 2.9 24.1 + - - -
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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