Contacts of the strand formed by residues 301 - 306 (chain A) in PDB entry 3VI4
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 ASP 301 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A PHE* 4.1 3.8 - - - -
291A ALA* 3.4 6.8 - - - +
292A THR 2.8 34.1 + - - +
293A ASP* 3.0 1.2 - - - +
294A VAL* 2.8 34.4 + - + +
295A ASN* 2.9 3.6 - - - +
299A LEU 3.3 1.4 - - - +
300A ASP* 1.3 73.9 - - - +
302A LEU* 1.3 62.8 + - - +
303A LEU* 4.0 2.7 + - + +
326A VAL* 5.0 2.5 - - + -
327A TYR 3.6 11.2 - - - +
328A LEU* 3.5 17.3 - - + +
329A GLN* 3.0 20.3 + - - +
2002A CA 2.3 30.2 - - - -
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Residues in contact with LEU 302 (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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240A PHE* 4.2 10.2 - - + -
249A VAL* 3.8 33.2 - - + -
262A VAL* 4.6 3.6 - - + -
264A ILE* 4.1 8.5 - - + -
276A PHE* 3.4 48.0 - - + -
290A ALA 3.8 11.7 - - - +
301A ASP* 1.3 73.9 - - - +
303A LEU* 1.3 78.4 + - - +
304A VAL* 4.2 16.6 - - + -
325A TYR 3.7 1.0 - - - +
326A VAL* 3.3 0.7 - - - +
327A TYR* 2.7 51.2 + - + +
334A ILE* 5.3 2.2 - - + -
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Residues in contact with LEU 303 (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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289A VAL* 3.4 6.1 - - - +
290A ALA* 3.1 52.8 + - + +
292A THR* 4.0 12.1 - - + -
294A VAL* 4.9 7.2 - - + -
301A ASP 4.6 6.7 - - - +
302A LEU* 1.3 86.6 - - - +
304A VAL* 1.3 66.2 + - - +
324A VAL* 5.0 6.3 - - + -
325A TYR 3.4 2.7 - - - +
326A VAL* 3.5 35.0 - - + -
355A LEU* 4.0 9.9 - - + -
369A VAL* 3.6 38.4 - - + -
394A LEU* 4.7 5.4 - - + -
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Residues in contact with VAL 304 (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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262A VAL* 3.4 26.9 - - + -
276A PHE* 5.8 0.7 - - + -
285A PHE* 3.7 34.5 - - + -
286A GLY* 3.4 27.1 - - - +
288A ALA 3.8 2.5 - - - +
289A VAL* 4.2 3.1 - - + -
302A LEU* 4.2 17.0 - - + -
303A LEU* 1.3 79.9 - - - +
305A GLY* 1.3 62.6 + - - +
324A VAL* 3.2 7.3 - - - +
325A TYR* 2.9 42.5 + - + +
327A TYR* 4.4 7.9 - - + -
355A LEU* 4.2 4.0 - - - -
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Residues in contact with GLY 305 (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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284A TYR 3.1 4.7 - - - +
286A GLY 2.9 24.2 + - - -
287A TYR 3.3 5.8 + - - -
288A ALA 2.8 17.1 + - - -
304A VAL* 1.3 74.7 - - - +
306A ALA* 1.3 58.6 + - - -
307A PRO* 3.9 4.9 - - - -
323A ARG 4.0 3.1 - - - -
324A VAL* 4.1 4.3 - - - -
352A GLY* 3.5 23.6 - - - -
355A LEU* 4.0 2.2 - - - +
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Residues in contact with ALA 306 (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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283A SER* 3.3 21.1 - - - +
284A TYR 3.5 2.9 - - - -
285A PHE* 3.6 18.8 - - + -
305A GLY* 1.3 74.1 - - - -
307A PRO* 1.3 68.2 - - - +
308A LEU 3.2 3.9 + - - -
309A LEU* 3.5 5.5 + - + +
322A GLY* 3.4 1.0 - - - -
323A ARG 2.9 34.0 + - - +
325A TYR* 3.8 18.6 - - + +
352A GLY* 4.1 1.0 - - - -
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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