Contacts of the strand formed by residues 284 - 294 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I TYR* 3.7 24.7 + - + -
276I THR* 4.9 13.5 - - + -
277I LEU 4.3 0.2 - - - +
278I GLU* 3.6 11.0 - - + +
282I GLY 4.3 7.4 - - - +
283I GLN* 1.3 84.5 - - - +
285I LEU* 1.3 65.5 + - - +
286I GLY 3.4 29.4 - - - +
287I ARG* 4.2 24.2 - - + +
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Residues in contact with LEU 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I TYR* 3.5 6.5 - - - -
122I PRO 3.8 1.0 - - - +
123I GLY* 2.9 27.7 - - - -
124I PRO* 3.2 22.8 - - + +
125I HIS* 4.9 13.2 + - + +
127I PHE* 5.2 0.8 - - - +
169I PRO* 5.3 0.9 - - + -
170I PRO* 4.3 15.0 - - + -
173I THR* 4.2 11.2 - - - +
277I LEU* 3.0 18.3 + - + +
278I GLU* 4.1 6.3 - - - -
279I MET* 3.9 42.0 - - + +
283I GLN* 3.9 14.1 - - - +
284I VAL* 1.3 79.4 - - - +
286I GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I TYR* 3.2 14.8 - - - -
122I PRO 4.2 0.2 - - - -
127I PHE* 3.6 21.8 - - - -
276I THR* 3.5 0.5 - - - -
277I LEU* 2.8 30.8 + - - +
284I VAL* 3.4 8.1 - - - +
285I LEU* 1.3 83.1 - - - +
287I ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I SER* 3.1 48.6 + - - -
118I ASN* 4.5 1.3 - - - +
119I THR* 2.8 39.9 + - - +
120I ASP* 3.5 1.0 - - - -
121I TYR* 2.7 49.3 + - + +
127I PHE* 3.6 2.5 - - - -
274I ILE* 3.5 18.6 - - + -
275I ILE 3.5 12.6 - - - +
276I THR* 3.9 10.5 - - + -
284I VAL* 4.2 25.3 - - + +
286I GLY* 1.3 75.5 - - - +
288I ARG* 1.3 74.7 + - - +
289I SER* 5.6 0.2 - - - -
245L VAL* 4.6 7.9 - - - +
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Residues in contact with ARG 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN 4.6 0.2 + - - -
208B SER* 4.5 16.8 + - - +
209B ALA 5.3 3.2 + - - +
120I ASP* 2.9 40.6 + - - +
121I TYR 4.4 1.6 - - - +
122I PRO* 3.2 33.2 - - - +
127I PHE* 2.6 39.3 + - + +
128I GLU* 3.2 24.9 - - - +
129I VAL* 3.5 35.7 + - + +
274I ILE* 3.7 0.7 - - - +
275I ILE* 2.8 34.9 + - - +
287I ARG* 1.3 81.5 + - - +
289I SER* 1.3 61.6 + - - +
290I PHE* 5.3 1.1 - - + -
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Residues in contact with SER 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I ASN* 2.9 28.4 + - - -
119I THR 4.8 0.2 - - - -
120I ASP* 3.1 18.1 + - - +
272I LEU* 4.4 10.3 - - - +
273I ILE 3.4 6.3 - - - -
274I ILE* 3.5 26.7 - - - -
287I ARG* 5.6 0.2 - - - -
288I ARG* 1.3 75.9 - - - +
290I PHE* 1.3 75.0 + - - +
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Residues in contact with PHE 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I VAL* 4.0 15.9 - - + -
131I PHE* 3.5 36.6 - + - -
144I TYR* 4.7 9.0 - + + +
149I LYS* 3.8 15.3 - - + +
151I LEU* 4.0 24.2 - - + -
161I ILE* 4.7 6.7 - - + -
256I PHE* 6.1 0.7 - + - -
272I LEU* 3.3 10.6 - - - +
273I ILE* 2.6 55.6 + - + -
275I ILE* 3.6 31.9 - - + -
288I ARG 5.3 0.4 - - - -
289I SER* 1.3 86.6 - - - +
291I GLU* 1.3 65.6 + - - +
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Residues in contact with GLU 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148I LEU 5.2 4.1 - - - +
149I LYS 3.6 5.9 + - - +
150I LYS* 2.9 44.2 + - + +
151I LEU* 2.6 31.4 + - - -
182I LYS* 3.2 37.1 + - + +
270I PRO* 4.0 13.7 - - - +
271I ILE 3.3 16.6 - - - +
272I LEU* 3.9 11.6 - - + +
290I PHE* 1.3 78.4 - - - +
292I GLY* 1.3 61.1 + - - +
293I ARG* 5.8 0.2 - - - +
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Residues in contact with GLY 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I LYS* 4.9 0.4 - - - -
151I LEU* 3.2 13.5 - - - -
260I SER* 4.2 1.4 + - - -
270I PRO* 5.3 0.9 - - - +
271I ILE* 2.9 37.9 + - - +
273I ILE* 4.5 15.8 - - - +
290I PHE 3.8 2.2 + - - -
291I GLU* 1.3 81.8 - - - +
293I ARG* 1.3 60.7 + - - +
294I ILE* 4.1 4.3 - - - -
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Residues in contact with ARG 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I LYS* 4.0 19.3 - - - +
151I LEU 2.6 10.2 + - - -
152I TYR* 3.4 33.5 - - + -
153I CYS 3.2 17.5 + - - -
260I SER* 4.1 15.8 - - - -
261I SER* 5.7 3.0 - - - +
268I ARG* 6.3 1.4 - - - +
292I GLY* 1.3 74.3 - - - +
294I ILE* 1.3 63.3 + - - +
295I CYS* 3.1 19.7 + - + +
301I ASP* 2.7 36.1 + - - +
305I ASP* 4.9 3.7 + - - -
618N T 3.1 57.1 + - - +
619N G 5.5 1.4 + - - -
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Residues in contact with ILE 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I LEU* 5.6 1.6 - - + +
153I CYS* 3.2 19.7 - - + +
155I ILE* 4.0 22.2 - - - +
214I LEU* 5.0 0.2 - - + -
256I PHE* 3.2 48.2 - - + +
258I CYS 3.4 21.3 - - - +
259I ASN* 3.2 21.5 - - - +
260I SER* 2.7 37.5 + - - +
261I SER 4.5 1.2 + - - -
266I MET* 4.5 8.3 - - + -
271I ILE* 4.6 9.4 - - + -
273I ILE* 5.9 0.9 - - + -
292I GLY* 5.4 1.8 - - - -
293I ARG* 1.3 73.7 + - - +
295I CYS* 1.3 59.7 + - - +
619N G 4.6 0.7 + - - -
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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