Contacts of the strand formed by residues 284 - 295 (chain C) in PDB entry 3VD1
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 VAL 284 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B VAL* 3.8 35.2 - - + +
121C TYR* 4.1 6.5 + - + -
276C THR* 4.8 13.7 - - + +
277C LEU 4.1 2.9 - - - +
278C GLU* 4.8 3.8 - - - +
282C GLY 3.9 8.3 - - - +
283C GLN* 1.3 81.6 - - - +
285C LEU* 1.3 65.4 + - - +
286C GLY 3.7 23.8 - - - +
287C ARG* 4.0 24.9 - - - +
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C TYR* 3.7 7.3 - - - -
122C PRO 3.0 16.1 - - - +
123C GLY* 3.5 12.5 - - - -
124C PRO* 3.7 24.9 - - + +
125C HIS* 4.3 11.5 + - + +
170C PRO* 3.7 24.5 - - + -
173C THR* 4.5 10.8 - - + +
277C LEU* 2.9 28.6 + - + +
278C GLU 4.7 0.9 - - - +
279C MET* 3.1 39.5 - - + -
283C GLN* 3.8 3.8 + - + +
284C VAL* 1.3 77.5 - - - +
286C GLY* 1.3 58.6 + - - +
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Residues in contact with GLY 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C TYR* 3.4 12.6 - - - -
122C PRO 3.7 6.3 - - - -
127C PHE* 3.9 5.2 - - - -
276C THR* 3.6 5.2 + - - -
277C LEU* 3.0 36.3 + - - +
284C VAL* 3.7 10.8 - - - +
285C LEU* 1.3 80.5 - - - +
287C ARG* 1.3 66.4 + - - +
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLN* 4.5 6.3 + - - +
245B VAL 2.6 30.6 + - - +
246B GLY* 4.2 6.4 - - - -
117C SER* 2.9 54.8 + - - -
118C ASN 4.3 1.3 - - - -
119C THR* 2.9 30.3 + - - +
120C ASP* 3.4 0.6 - - - -
121C TYR* 3.1 33.0 + - + +
127C PHE* 3.4 6.8 - - - -
274C ILE* 3.7 20.4 - - + -
275C ILE 3.3 9.2 - - - +
276C THR* 3.8 12.6 + - - +
284C VAL* 4.0 19.3 - - + +
286C GLY* 1.3 76.6 - - - +
288C ARG* 1.3 78.4 + - - +
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Residues in contact with ARG 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ASN 5.0 0.2 - - - -
120C ASP* 3.4 32.7 + - - +
122C PRO* 3.5 33.1 - - - +
127C PHE* 3.0 39.8 + - + +
128C GLU* 3.6 21.7 + - - +
129C VAL* 3.5 35.9 - - + +
274C ILE* 3.5 3.5 - - - +
275C ILE* 3.0 33.0 + - + +
287C ARG* 1.3 84.1 + - - +
289C SER* 1.3 63.9 + - - +
290C PHE* 5.1 1.1 - - - -
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Residues in contact with SER 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASN* 3.0 24.8 + - - +
120C ASP* 3.3 9.2 + - - +
129C VAL* 5.5 1.4 - - - +
149C LYS* 3.6 21.1 + - - +
272C LEU* 3.3 23.1 - - - +
273C ILE 3.5 10.1 - - - -
274C ILE* 4.1 9.6 - - - -
288C ARG* 1.3 78.7 - - - +
290C PHE* 1.3 73.4 + - - +
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Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C VAL* 4.7 12.6 - - + -
131C PHE* 4.0 28.9 - + + -
144C TYR* 4.7 5.4 - + + +
149C LYS* 3.4 24.2 - - + +
151C LEU* 3.8 32.8 - - + -
161C ILE* 5.1 6.3 - - + -
256C PHE* 6.0 1.1 - + - -
272C LEU* 3.2 9.1 - - - +
273C ILE* 2.9 62.5 + - + -
275C ILE* 4.1 21.8 - - + -
288C ARG 5.3 0.2 - - - -
289C SER* 1.3 87.4 + - - +
291C GLU* 1.3 71.7 + - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU 5.0 3.7 - - - +
149C LYS 3.0 11.5 + - - +
150C LYS* 3.2 40.5 + - + -
151C LEU 2.8 25.5 + - - -
182C LYS* 3.4 37.5 + - + +
270C PRO* 3.7 19.0 - - + +
271C ILE 3.1 21.8 - - - +
272C LEU* 4.1 4.6 - - + +
290C PHE* 1.3 78.4 - - - +
292C GLY* 1.3 61.6 + - - +
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Residues in contact with GLY 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LYS* 4.7 1.5 - - - +
151C LEU* 3.7 10.5 - - - -
260C SER* 3.9 1.7 + - - -
270C PRO* 4.8 3.5 - - - +
271C ILE* 3.3 45.9 + - - +
272C LEU* 4.3 0.6 - - - +
273C ILE* 5.0 7.9 - - - -
290C PHE* 3.8 1.8 + - - -
291C GLU* 1.3 78.7 - - - +
293C ARG* 1.3 61.8 + - - +
294C ILE* 4.3 2.9 - - - -
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LYS* 4.2 25.7 - - + +
151C LEU 3.1 9.8 + - - +
152C TYR* 3.6 19.4 - - + -
153C CYS 3.4 19.2 + - - -
260C SER* 2.8 20.8 - - - +
292C GLY* 1.3 75.1 - - - +
294C ILE* 1.3 65.9 + - - +
295C CYS* 3.4 20.4 - - - +
301C ASP* 2.8 32.3 + - - -
305C ASP* 4.8 6.5 + - - -
505G A 5.3 0.2 - - - +
506G T 2.6 53.7 + - - +
507G G 4.9 1.8 + - - -
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C CYS* 3.1 17.3 - - + +
154C GLN 3.6 22.0 - - - +
155C ILE* 3.9 3.1 - - - +
256C PHE* 3.5 41.3 - - + -
258C CYS 3.1 29.4 - - - +
259C ASN* 3.5 13.0 - - - +
260C SER* 2.5 32.6 + - - +
266C MET* 3.7 17.0 - - + -
271C ILE* 5.1 6.1 - - + -
292C GLY* 5.2 1.3 - - - -
293C ARG* 1.3 83.1 + - - +
295C CYS* 1.3 60.7 + - - +
507G G 4.0 4.3 + - - -
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Residues in contact with CYS 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C TYR* 4.2 4.3 - - - -
153C CYS 2.9 10.9 + - - -
154C GLN* 3.6 18.0 - - - +
155C ILE* 3.9 2.8 + - - +
259C ASN* 3.1 16.8 - - - +
293C ARG* 3.4 32.5 - - - +
294C ILE* 1.3 74.5 - - - +
296C ALA* 1.3 63.6 + - - +
297C CYS 3.3 11.0 - - - +
298C PRO* 4.1 15.5 - - + -
301C ASP* 3.5 33.9 - - - +
507G G 3.6 8.7 - - - +
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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