Contacts of the strand formed by residues 170 - 175 (chain A) in PDB entry 3F4V
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 HIS 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A THR* 3.7 28.0 - - + +
124A PRO 3.7 5.4 + - - +
125A TYR* 3.4 47.3 + + + -
126A VAL 2.9 23.4 + - - -
168A VAL* 3.7 4.8 - - - +
169A LYS* 1.3 95.9 + - + +
171A TRP* 1.3 61.7 + - - +
237A LYS* 5.1 7.8 - - + +
309A TYR* 3.3 25.6 - + - +
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Residues in contact with TRP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 4.3 2.5 - - + -
126A VAL* 3.3 38.1 - - + -
128A LEU* 3.8 30.7 - - + -
160A CYS* 3.5 32.5 - - + -
161A PHE* 3.6 25.2 - + + -
164A PHE* 3.9 13.2 - + + -
165A GLY* 3.9 11.9 - - - -
168A VAL* 3.5 37.1 + - + -
169A LYS 4.5 1.6 - - - -
170A HIS* 1.3 78.3 - - - +
172A PHE* 1.3 64.2 + - - +
226A TYR* 4.1 13.6 + + - -
237A LYS 3.0 23.7 + - - +
238A VAL* 3.9 22.9 - - + -
239A GLY 2.9 16.8 + - - -
309A TYR* 2.8 16.7 + - - -
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Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG* 4.2 7.6 - - - -
125A TYR* 4.0 34.5 - + + -
126A VAL 2.8 16.6 + - - +
127A ASN* 3.3 30.3 - - - +
128A LEU* 2.9 31.1 + - - +
170A HIS 5.3 0.2 - - - -
171A TRP* 1.3 78.1 - - - +
173A THR* 1.3 61.5 + - - +
174A PHE 4.5 1.8 - - - +
239A GLY 3.3 7.0 - - - +
240A ILE 3.7 15.5 - - - -
241A VAL* 3.5 15.3 - - + -
309A TYR* 3.3 31.2 - + - -
311A GLY* 4.3 7.4 - - - -
383A VAL* 4.9 5.2 - - + -
385A THR* 3.5 32.3 - - + -
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Residues in contact with THR 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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127A ASN* 3.6 0.4 + - - -
128A LEU* 3.4 8.8 + - + +
129A TYR* 3.0 31.4 + - - +
153A PHE* 3.9 26.2 - - + -
161A PHE* 5.9 0.2 - - + -
172A PHE* 1.3 74.9 - - - +
174A PHE* 1.3 82.3 + - - +
219A HIS* 2.7 35.5 + - + +
222A ALA* 4.4 11.4 - - + -
238A VAL* 3.8 20.9 - - + -
239A GLY 3.0 9.4 + - - -
240A ILE* 3.7 4.3 - - - +
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 3.3 14.9 + - - -
129A TYR* 3.7 18.2 - + + -
144A TRP* 3.4 34.1 - + - -
153A PHE* 3.5 38.6 - + - -
172A PHE* 4.5 0.2 - - - +
173A THR* 1.3 87.7 + - - +
175A ASN* 1.3 60.8 + - - +
177A PRO* 4.5 8.5 - - + -
215A PHE* 3.4 51.1 - + + -
218A SER* 3.8 4.7 - - - -
219A HIS* 3.6 15.9 - - + -
240A ILE* 4.1 17.4 - - + +
241A VAL* 3.0 25.9 + - - +
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Residues in contact with ASN 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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86A ARG* 2.8 24.1 + - - +
127A ASN* 3.9 0.2 - - - +
129A TYR* 3.5 16.9 + - - +
130A HIS* 3.2 36.9 + - + +
131A TYR* 3.4 20.0 + - - -
174A PHE* 1.3 76.0 - - - +
176A GLN* 1.3 80.0 + - - +
177A PRO* 3.4 3.1 - - - +
180A VAL* 4.4 2.1 - - - +
241A VAL* 3.3 4.0 - - - +
313A ASN* 3.2 18.4 + - - -
1004A GOL 2.8 22.1 + - - -
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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