Contacts of the strand formed by residues 168 - 174 (chain A) in PDB entry 3FZF
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 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 2.8 18.8 + - - +
141A ASN* 3.2 28.0 + - - +
142A ALA 3.2 18.2 + - - -
167A LEU* 1.3 71.4 - - - +
169A VAL* 1.3 63.0 + - - +
170A LEU* 3.0 27.6 + - - +
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Residues in contact with VAL 169 (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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142A ALA 3.4 8.1 - - - +
144A VAL* 4.3 16.8 - - + -
158A THR 5.5 0.2 - - - +
159A LYS* 4.2 30.0 - - + +
162A GLY* 4.2 24.9 - - - -
163A THR* 4.5 2.6 + - - +
167A LEU* 3.5 10.3 + - + +
168A ASN* 1.3 73.8 + - - +
170A LEU* 1.3 67.7 + - - +
171A ARG* 3.2 28.9 + - - +
172A ILE* 3.9 20.6 - - + -
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Residues in contact with LEU 170 (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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6A ALA* 4.3 3.6 - - + -
141A ASN* 3.8 29.2 - - + +
142A ALA 2.9 14.4 + - - +
143A VAL* 4.3 4.0 - - + -
168A ASN* 3.0 32.9 + - - +
169A VAL* 1.3 72.6 - - - +
171A ARG* 1.3 66.8 + - - +
377A ALA* 3.5 31.6 - - + +
380A LEU* 3.8 33.7 - - + +
381A SER* 3.9 7.0 - - - +
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Residues in contact with ARG 171 (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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142A ALA 4.1 0.6 + - - -
143A VAL* 3.5 7.2 - - + +
144A VAL 3.3 22.9 + - - +
169A VAL* 3.1 12.9 - - - +
170A LEU* 1.3 83.8 + - - +
172A ILE* 1.3 72.3 + - - +
173A ILE* 3.5 24.4 - - + +
376A GLN* 4.1 11.5 + - - -
380A LEU* 4.0 40.8 - - + +
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Residues in contact with ILE 172 (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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144A VAL* 3.2 18.4 - - + +
146A VAL* 3.6 33.2 - - + -
155A ARG* 4.1 26.4 + - + +
158A THR* 4.2 13.2 - - + +
159A LYS* 4.2 32.5 - - + +
169A VAL* 3.9 21.8 - - + -
171A ARG* 1.3 82.0 - - - +
173A ILE* 1.3 62.1 + - - +
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Residues in contact with ILE 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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143A VAL* 3.5 25.4 - - + -
144A VAL 3.2 5.7 + - - -
145A THR* 2.9 31.1 - - + -
146A VAL* 3.1 4.6 + - - -
171A ARG* 3.5 30.5 - - + +
172A ILE* 1.3 70.7 - - - +
174A ASN* 1.3 75.4 + - - +
177A THR* 3.8 22.2 - - + -
178A ALA* 3.8 14.4 - - + +
181A ILE* 4.8 5.2 - - + -
373A ALA* 5.4 2.0 - - - -
376A GLN* 3.5 35.2 - - + -
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Residues in contact with ASN 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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146A VAL* 3.1 6.7 - - - +
147A PRO 3.7 1.4 - - - +
148A ALA* 3.6 12.5 + - - +
155A ARG* 2.7 39.7 + - - +
172A ILE 4.5 0.2 + - - -
173A ILE* 1.3 75.8 - - - +
175A GLU* 1.3 66.1 + - - +
176A PRO* 3.9 14.8 - - + -
177A THR* 3.1 16.9 + - - +
178A ALA* 3.0 19.1 + - - +
219A VAL* 3.5 27.7 - - - +
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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