Contacts of the strand formed by residues 119 - 123 (chain A) in PDB entry 3FZ7
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 VAL 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A PRO* 6.1 1.3 - - + -
117A GLN 4.7 4.3 - - - +
118A ALA* 1.3 75.0 - - - +
120A GLY* 1.3 59.0 + - - +
288A ILE* 3.4 7.6 - - - +
289A TRP* 3.0 47.1 + - + +
291A ASP* 3.8 6.7 - - - +
292A GLU* 3.5 51.4 - - + +
295A LEU* 3.8 32.8 - - + -
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Residues in contact with GLY 120 (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 LEU* 6.1 0.5 - - - +
101A VAL* 3.9 21.0 - - - +
118A ALA 3.7 3.9 + - - +
119A VAL* 1.3 77.9 - - - +
121A THR* 1.3 65.7 + - - -
287A VAL 3.1 13.9 - - - -
288A ILE* 4.1 1.1 - - - -
289A TRP* 3.7 10.7 - - - -
295A LEU* 5.8 0.2 - - - +
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Residues in contact with THR 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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84A TRP* 3.8 16.3 - - - -
101A VAL* 4.1 6.5 - - - +
120A GLY* 1.3 77.7 - - - -
122A ASN* 1.3 81.4 + - - +
123A THR* 4.2 0.2 - - + -
132A LEU* 3.8 9.2 - - + -
286A TRP* 3.6 7.2 - - - -
287A VAL* 2.8 52.5 + - + +
288A ILE* 4.6 0.4 - - - +
289A TRP* 4.3 7.0 - - + -
313A PHE* 3.7 27.2 + - + +
314A ALA* 5.4 0.6 - - - +
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Residues in contact with ASN 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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84A TRP* 3.6 10.1 - - - +
97A ASP* 3.2 23.6 + - - +
101A VAL* 4.2 2.6 - - - +
121A THR* 1.3 93.7 + - - +
123A THR* 1.3 65.5 + - - +
128A GLU* 5.4 0.5 - - - -
283A GLY 5.0 1.0 - - - +
284A CYS* 3.3 15.8 - - - -
285A GLY 3.1 22.0 + - - -
286A TRP* 3.2 32.5 - - + -
319A ARG* 2.8 40.9 + - - -
324A VAL* 3.3 18.3 - - - +
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Residues in contact with THR 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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121A THR* 4.1 8.7 - - + +
122A ASN* 1.3 88.6 - - - +
124A ILE* 1.3 56.8 + - - +
125A GLY 2.6 25.9 + - - -
128A GLU* 3.3 32.3 - - + +
129A ALA* 3.7 18.1 - - + +
132A LEU* 3.9 13.2 - - + -
283A GLY 3.9 0.7 - - - +
284A CYS* 3.4 4.2 - - - -
285A GLY 2.7 38.8 + - - -
286A TRP 3.6 0.7 + - - -
287A VAL* 4.2 0.7 - - + -
319A ARG* 3.6 9.9 - - - +
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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