Contacts of the strand formed by residues 119 - 124 (chain A) in PDB entry 5FWV
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 ASN 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ALA 5.1 7.3 + - - -
115A GLN* 3.3 33.3 - - + +
116A MET* 2.8 32.8 + - + +
117A PRO* 3.4 1.0 + - - +
118A GLY* 1.3 70.7 + - - +
120A LEU* 1.3 59.8 + - - +
121A GLY* 3.0 22.7 + - - +
197A PRO* 5.9 0.2 - - - +
205A ILE* 3.8 24.3 - - - +
206A LEU 3.7 6.7 - - - +
207A PHE* 3.7 27.2 - - + -
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Residues in contact with LEU 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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115A GLN* 3.8 2.9 - - - +
118A GLY* 3.7 19.7 - - - +
119A ASN* 1.3 74.1 - - - +
121A GLY* 1.3 52.1 - - - +
123A TYR* 2.8 27.3 + - - -
158A PHE* 3.6 35.9 - - + -
175A TYR* 3.6 26.7 + - + +
180A GLU* 5.2 0.5 - - - +
206A LEU* 2.8 25.9 + - + +
207A PHE 4.2 2.7 - - - -
208A ASP* 4.0 15.3 - - + +
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 3.3 15.6 + - - -
119A ASN* 3.0 10.9 + - - +
120A LEU* 1.3 79.1 - - - +
122A CYS* 1.3 61.7 + - - -
123A TYR* 3.4 13.6 - - - -
180A GLU* 4.5 7.6 - - - -
205A ILE* 3.6 4.9 - - - -
206A LEU 3.1 24.4 + - - -
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Residues in contact with CYS 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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121A GLY* 1.3 72.9 - - - -
123A TYR* 1.3 62.8 + - - +
180A GLU* 3.2 11.2 + - - +
181A ALA* 2.7 45.3 + - - +
182A ALA 3.7 10.1 - - - -
183A SER* 4.0 13.2 - - - -
185A GLU 4.2 2.0 - - - -
186A CYS* 2.1 58.6 - - + -
203A ARG* 4.4 3.8 - - - -
204A ILE 3.5 3.6 - - - -
205A ILE* 5.2 1.6 - - + -
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Residues in contact with TYR 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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120A LEU 2.8 22.4 + - - -
121A GLY* 3.4 25.6 - - - -
122A CYS* 1.3 75.8 - - - +
124A LYS* 1.3 66.6 + - - +
175A TYR* 3.8 34.7 + + - +
176A TRP* 3.5 32.8 - - + +
179A GLY 3.6 5.4 - - - +
180A GLU* 3.5 39.8 - - + +
181A ALA* 4.1 1.1 - - - +
203A ARG* 3.3 8.5 - - - -
204A ILE* 2.8 43.8 + - + +
206A LEU* 4.2 12.6 - - + -
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Residues in contact with LYS 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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123A TYR* 1.3 76.9 - - - +
125A ASP* 1.3 58.9 + - - +
126A HIS* 4.0 22.6 - - + +
131A PRO* 4.0 10.4 - - - +
175A TYR 4.8 0.5 - - - +
178A TYR* 3.4 40.5 + - - +
179A GLY* 3.0 14.0 + - - +
180A GLU 4.0 15.0 - - - -
181A ALA* 4.3 6.5 - - + +
185A GLU* 5.5 1.1 - - - -
202A GLY 3.6 5.8 - - - -
203A ARG* 3.7 35.5 - - - +
1323A CL 4.3 7.5 - - + +
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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