Contacts of the strand formed by residues 172 - 177 (chain A) in PDB entry 5FJV
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 LYS 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A MET* 4.7 0.3 - - - +
123A ASN* 3.1 40.7 + - - +
155A SER* 4.3 2.4 + - - -
156A SER 4.0 8.2 + - - +
157A CYS* 5.0 0.8 - - - +
158A SER 5.6 0.2 - - - +
170A ASN* 3.5 16.1 + - - +
171A CYS* 1.3 75.3 - - - +
173A MET* 1.3 64.1 + - - +
174A LYS* 4.7 15.3 - - + +
230A THR* 4.3 17.7 - - + +
231A TYR 3.1 12.6 - - - +
232A ALA* 4.7 1.3 - - + +
201B GLU* 2.4 44.9 + - - -
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Residues in contact with MET 173 (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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64A LEU* 4.3 6.1 - - - -
79A MET* 4.5 4.5 - - + -
81A THR* 4.2 16.4 - - - +
83A VAL* 4.9 6.7 - - + -
121A LEU* 3.5 13.5 - - + -
123A ASN* 4.2 3.8 - - - -
153A TYR* 4.0 25.6 - - + -
155A SER* 4.0 14.8 - - - +
171A CYS 4.0 0.2 + - - -
172A LYS* 1.3 78.3 - - - +
174A LYS* 1.3 60.5 + - - +
175A PHE* 3.2 38.9 + - + -
230A THR* 3.4 2.3 - - - -
231A TYR* 2.7 47.7 + - + +
233A PHE* 4.0 25.4 - - + -
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Residues in contact with LYS 174 (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 LEU* 3.2 3.9 - - - +
122A TYR* 2.4 78.1 + - + -
123A ASN* 3.3 16.1 + - + +
172A LYS* 4.2 16.8 - - - +
173A MET* 1.3 71.4 - - - +
175A PHE* 1.3 59.2 + - - +
217A LYS* 5.7 2.4 - - - +
219A TYR* 3.4 25.3 + - - -
228A ASP* 3.8 25.8 - - - +
230A THR* 3.3 27.6 - - + +
199B TYR* 4.8 9.1 - - - -
201B GLU* 5.4 2.0 + - - +
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Residues in contact with PHE 175 (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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62A PHE* 3.6 31.2 - + + -
64A LEU* 3.6 37.2 - - + -
85A LEU* 3.8 18.8 - - + -
119A ILE* 4.4 4.7 - - + -
120A VAL 3.2 14.4 - - - +
121A LEU* 3.6 13.2 - - + -
122A TYR* 4.3 2.7 - - - -
153A TYR* 3.5 30.1 - + - -
173A MET* 3.2 44.2 - - + -
174A LYS* 1.3 73.2 - - - +
176A GLY* 1.3 58.6 + - - +
187A LEU* 5.6 0.2 - - - -
228A ASP* 3.3 7.1 - - - +
229A VAL 3.0 31.5 + - - +
231A TYR* 4.2 9.0 - + - -
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Residues in contact with GLY 176 (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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119A ILE* 3.5 11.9 - - - +
120A VAL* 2.7 37.1 + - - +
122A TYR* 3.9 15.2 - - - -
175A PHE* 1.3 74.4 - - - +
177A SER* 1.3 65.9 + - - -
178A TRP 3.5 0.2 + - - -
187A LEU* 4.6 4.0 - - - -
227A PRO 4.2 11.9 - - - -
228A ASP* 4.3 2.2 - - - -
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Residues in contact with SER 177 (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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117A PRO* 5.8 0.7 - - - -
118A ASP* 2.7 32.8 + - - -
119A ILE* 3.3 15.2 - - - +
122A TYR* 3.7 11.8 + - - -
176A GLY* 1.3 74.0 - - - -
178A TRP* 1.3 62.9 + - - +
180A TYR* 3.0 36.9 + - - +
185A ILE* 4.8 13.5 - - - -
187A LEU* 4.9 3.0 - - - +
226A TYR* 4.5 3.8 - - - +
227A PRO* 4.4 10.5 + - - +
300A EPJ 4.2 0.3 + - - -
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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