Contacts of the strand formed by residues 284 - 295 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121L TYR* 3.5 20.9 + - + -
276L THR* 4.1 17.0 - - + -
277L LEU 3.9 3.8 - - - +
278L GLU* 4.6 4.3 - - + +
282L GLY 4.3 5.6 - - - +
283L GLN* 1.3 78.9 - - - +
285L LEU* 1.3 66.4 + - - +
286L GLY 3.9 22.7 - - - +
287L ARG* 4.1 26.0 - - + +
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Residues in contact with LEU 285 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L TYR* 3.6 6.1 - - - -
122L PRO 3.9 1.9 - - - +
123L GLY* 3.2 22.7 - - - -
124L PRO* 3.4 13.8 - - + +
125L HIS* 4.2 17.9 + - + +
127L PHE* 5.0 0.2 - - - +
169L PRO* 4.4 0.4 - - + -
170L PRO* 4.2 11.4 - - + -
173L THR* 3.9 34.5 - - + -
277L LEU* 2.9 31.0 + - + +
278L GLU 4.4 7.0 - - - -
279L MET* 3.4 31.0 - - + -
283L GLN* 4.1 10.5 - - + +
284L VAL* 1.3 80.8 - - - +
286L GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 286 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L TYR* 3.1 18.3 - - - -
122L PRO 4.4 0.2 - - - -
127L PHE* 3.5 21.0 - - - -
276L THR* 3.1 4.7 - - - -
277L LEU* 2.7 31.9 + - - +
284L VAL* 3.5 2.9 - - - +
285L LEU* 1.3 81.6 - - - +
287L ARG* 1.3 61.8 + - - +
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Residues in contact with ARG 287 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L SER* 2.6 33.7 + - - -
118L ASN* 3.4 18.8 - - - +
119L THR* 2.5 51.6 + - - +
120L ASP* 3.6 1.9 - - - -
121L TYR* 2.8 49.7 + - + +
127L PHE* 3.7 2.5 - - - -
274L ILE* 3.4 19.5 - - + -
275L ILE 3.2 5.2 - - - -
276L THR* 3.5 19.0 - - + +
284L VAL* 4.1 22.6 - - + +
286L GLY* 1.3 76.0 - - - +
288L ARG* 1.3 70.4 + - - +
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Residues in contact with ARG 288 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L ASN* 4.5 2.5 - - - -
120L ASP* 4.2 25.4 + - - +
121L TYR 4.9 0.4 - - - +
122L PRO* 3.4 35.2 - - - +
126L HIS* 5.0 2.2 - - - +
127L PHE* 2.9 32.4 + - + +
128L GLU* 3.9 18.5 + - - +
129L VAL* 4.1 31.2 - - + +
274L ILE* 3.7 2.6 - - - +
275L ILE* 2.8 32.2 + - - +
287L ARG* 1.3 82.5 + - - +
289L SER* 1.3 65.0 + - - +
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Residues in contact with SER 289 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L ASN* 2.7 33.4 + - - +
120L ASP* 4.9 7.4 + - - -
149L LYS* 3.8 16.2 + - - -
272L LEU* 4.2 13.1 - - - +
273L ILE 3.0 21.5 - - - -
274L ILE* 4.0 0.2 - - - -
288L ARG* 1.3 77.4 - - - +
290L PHE* 1.3 77.7 + - - +
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Residues in contact with PHE 290 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L VAL* 3.7 23.1 - - + -
131L PHE* 3.6 32.3 - + - -
144L TYR* 4.3 5.6 - - + +
149L LYS* 3.8 27.1 - - + +
151L LEU* 3.8 26.2 - - + -
161L ILE* 4.2 12.6 - - + -
254L TYR* 6.2 0.2 - + - -
256L PHE* 5.3 1.6 - + - -
272L LEU* 3.8 6.3 - - - -
273L ILE* 2.9 62.4 + - + -
275L ILE* 3.9 16.6 - - + -
289L SER* 1.3 87.6 + - - +
291L GLU* 1.3 65.2 + - - +
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Residues in contact with GLU 291 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L LEU* 4.1 11.3 - - + +
149L LYS* 4.0 9.6 - - + +
150L LYS* 3.0 46.8 + - + +
151L LEU* 2.7 27.0 + - - +
182L LYS* 3.4 30.2 + - + +
270L PRO* 3.2 29.3 - - - +
271L ILE 3.3 12.8 - - - +
272L LEU* 3.8 12.5 - - + +
290L PHE* 1.3 77.2 - - - +
292L GLY* 1.3 67.6 + - - +
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Residues in contact with GLY 292 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L LYS* 5.3 0.2 - - - -
151L LEU* 3.4 9.2 - - - -
260L SER* 4.5 0.9 + - - -
266L MET* 5.3 0.2 - - - +
270L PRO* 4.6 3.6 - - - +
271L ILE* 3.0 35.5 + - - +
273L ILE* 4.0 21.0 - - - +
290L PHE 3.7 1.6 + - - -
291L GLU* 1.3 81.7 - - - +
293L ARG* 1.3 62.7 + - - +
294L ILE* 4.3 3.6 - - - -
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Residues in contact with ARG 293 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L LYS* 4.0 25.0 - - - +
151L LEU 2.9 9.3 + - - +
152L TYR* 3.5 25.8 - - + -
153L CYS 3.4 15.8 + - - -
260L SER* 3.1 21.8 - - - +
261L SER 5.8 1.6 - - - +
270L PRO* 6.4 0.9 - - + -
292L GLY* 1.3 75.1 - - - +
294L ILE* 1.3 61.4 + - - +
295L CYS* 2.9 31.0 + - - +
301L ASP* 2.8 31.1 + - - +
305L ASP* 4.6 2.9 + - - -
718P T 2.7 52.7 + - - -
719P G 5.6 1.5 + - - -
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Residues in contact with ILE 294 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L LEU* 5.9 1.1 - - + -
153L CYS* 3.1 12.1 - - + +
155L ILE* 3.6 22.2 - - - +
214L LEU* 5.7 1.1 - - + -
256L PHE* 3.3 46.2 - - + -
258L CYS 2.8 24.9 - - - +
259L ASN* 2.7 54.4 - - - +
260L SER* 2.5 25.9 + - - +
266L MET* 5.3 3.4 - - + -
271L ILE* 4.9 12.1 - - + -
273L ILE* 5.7 0.9 - - + -
292L GLY* 4.6 4.0 - - - -
293L ARG* 1.3 78.6 - - - +
295L CYS* 1.3 54.8 + - - +
719P G 4.1 1.7 + - - -
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Residues in contact with CYS 295 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L TYR* 4.5 0.9 - - + -
153L CYS 2.9 6.1 + - - -
154L GLN* 3.5 22.5 - - - +
155L ILE* 5.2 0.3 - - - +
259L ASN* 3.7 6.6 - - - +
293L ARG* 2.9 50.0 + - + +
294L ILE* 1.3 75.1 - - - +
296L ALA* 1.3 64.1 + - - +
298L PRO* 3.6 23.3 - - + +
301L ASP* 2.7 33.2 - - - +
719P G 3.5 8.5 - - - -
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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