Contacts of the strand formed by residues 271 - 279 (chain A) in PDB entry 3HFV
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 ARG 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASP* 2.7 44.2 + - - -
163A LEU* 3.8 27.2 - - + +
164A PHE 3.2 15.0 - - - +
165A SER* 3.6 22.6 - - - +
168A GLU* 5.6 1.6 + - - -
181A LEU* 4.3 0.7 - - - -
182A PHE* 3.7 5.3 - - - -
260A GLN* 3.0 26.5 + - - +
263A VAL* 3.8 5.9 - - + +
268A ALA* 3.2 16.8 + - + +
269A GLN 3.4 0.4 - - - -
270A ASP* 1.3 115.3 + - - +
272A ILE* 1.3 61.5 + - - +
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Residues in contact with ILE 272 (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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163A LEU* 4.2 2.2 - - - -
164A PHE* 2.5 55.6 + - + +
169A LEU* 4.3 0.4 - - + -
181A LEU* 4.0 25.1 - - + +
182A PHE* 5.1 1.1 - - + -
195A HIS* 3.7 42.8 - - + +
199A ALA* 4.1 23.1 - - + -
200A VAL* 4.9 0.9 - - + +
203A VAL* 3.6 31.0 - - + -
257A VAL* 4.3 7.6 - - + -
258A MET 5.7 0.4 - - - +
260A GLN* 4.2 3.6 - - - +
263A VAL* 5.5 0.9 - - - -
271A ARG* 1.3 74.3 - - - +
273A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 273 (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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162A ARG 3.0 13.2 - - - -
163A LEU* 4.0 12.0 - - - +
164A PHE* 4.6 1.6 - - - -
203A VAL* 3.9 6.6 - - - +
257A VAL* 3.5 11.5 - - - +
258A MET* 3.0 31.6 + - - +
260A GLN* 5.2 0.2 + - - -
263A VAL* 5.1 3.8 - - - +
272A ILE* 1.3 79.0 - - - +
274A TRP* 1.3 61.2 + - - +
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Residues in contact with TRP 274 (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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61A PHE* 4.7 1.8 - + - -
74A PHE* 4.2 13.7 - + - -
160A ALA* 3.8 15.5 - - + -
161A VAL* 3.5 0.2 - - - -
162A ARG* 3.0 59.1 + - + +
164A PHE* 3.8 15.7 - + - -
203A VAL* 3.6 29.4 - - + -
206A ASP* 2.7 26.9 + - - -
207A LEU* 3.6 33.9 - - + +
210A THR* 4.1 22.2 - - + -
256A GLY 3.3 14.4 - - - +
258A MET* 3.5 7.6 - - - +
273A GLY* 1.3 75.5 - - - +
275A ALA* 1.3 69.3 + - - +
276A PHE* 3.6 31.0 - + - -
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Residues in contact with ALA 275 (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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124A GLN* 3.8 14.1 - - - +
160A ALA 3.0 13.2 - - - +
161A VAL* 4.2 2.7 - - + -
207A LEU* 4.1 1.4 - - - +
235A THR* 4.8 2.7 - - + -
255A CYS* 3.1 4.5 - - - +
256A GLY 3.0 31.4 + - - +
258A MET* 3.9 19.0 - - + +
274A TRP* 1.3 79.2 - - - +
276A PHE* 1.3 61.2 + - - +
416A MTY 3.4 20.1 - - + +
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Residues in contact with PHE 276 (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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57A VAL* 5.5 0.4 - - + -
61A PHE* 4.3 19.5 - + - -
158A LEU* 3.9 19.1 - - + -
159A GLU* 3.4 2.3 - - - -
160A ALA* 3.0 52.6 + - + -
207A LEU* 4.1 1.8 - - + -
210A THR* 5.5 1.1 - - + -
211A LEU* 3.4 36.3 - - + -
214A LEU* 4.9 2.0 - - + -
253A LEU* 4.6 2.7 - - + -
254A GLY 3.1 6.5 - - - +
255A CYS* 3.2 24.2 - - + -
274A TRP* 3.6 29.2 - + - -
275A ALA* 1.3 71.4 - - - +
277A GLY* 1.3 65.3 + - - +
278A LEU* 3.4 31.2 - - + -
416A MTY 3.4 13.5 + - - -
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Residues in contact with GLY 277 (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 THR* 5.2 0.7 - - - -
157A GLN* 5.2 7.1 + - - -
158A LEU 3.5 7.2 - - - -
159A GLU* 3.6 14.4 - - - -
253A LEU* 3.1 3.8 - - - +
254A GLY 2.8 32.8 + - - -
276A PHE* 1.3 74.6 - - - +
278A LEU* 1.3 60.6 + - - -
279A GLY 4.3 0.2 + - - -
416A MTY 3.3 16.6 - - - +
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Residues in contact with LEU 278 (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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57A VAL* 5.2 6.7 - - + -
157A GLN* 3.2 9.4 - - - +
158A LEU* 3.0 49.9 + - + +
211A LEU* 5.0 0.2 - - + -
214A LEU* 4.6 16.6 - - + -
215A MET* 4.8 8.1 - - + -
252A VAL 3.5 13.9 - - - +
253A LEU* 3.6 10.8 - - + -
276A PHE* 3.4 27.6 - - + -
277A GLY* 1.3 74.2 - - - -
279A GLY* 1.3 63.0 + - - +
280A LEU* 3.5 28.0 - - + -
283A LEU* 3.9 24.2 - - + -
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Residues in contact with GLY 279 (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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155A PHE* 5.6 4.5 - - - -
156A HIS 3.6 7.0 - - - -
157A GLN* 4.6 7.9 - - - +
252A VAL 3.2 13.3 + - - +
253A LEU* 4.9 0.2 - - - +
277A GLY 4.3 0.2 + - - -
278A LEU* 1.3 70.5 - - - +
280A LEU* 1.3 66.7 + - - -
281A GLU* 3.3 3.4 - - - -
282A ARG* 3.5 12.1 + - - +
283A LEU* 3.1 24.1 + - - +
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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