Contacts of the strand formed by residues 350 - 362 (chain C) in PDB entry 3VZC
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 350 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C LEU* 3.8 30.3 - - + -
156C HIS 3.2 14.1 - - - +
157C THR* 4.4 8.7 - - + -
163C LEU* 5.9 0.2 - - + -
169C LEU* 3.9 13.7 - - + -
241C LEU* 4.8 3.8 - - - +
327C PHE* 4.1 5.4 - - + -
328C ARG* 3.5 0.3 - - - +
329C LEU* 2.7 41.8 + - + +
338C PHE* 3.6 38.6 - - + -
345C MET* 4.4 4.5 - - + -
347C SER* 4.0 8.5 - - - -
349C ALA* 1.3 80.7 - - - +
351C GLN* 1.3 60.1 + - - +
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Residues in contact with GLN 351 (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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155C LEU* 3.4 7.6 - - - +
156C HIS* 2.8 44.0 + - + +
238C LEU* 4.1 29.6 - - + +
239C VAL 3.2 20.3 + - - +
240C PRO* 4.4 1.2 - - - +
241C LEU* 3.7 29.3 + - + +
249C TRP* 4.8 3.4 - - - -
327C PHE* 3.1 19.1 - - - +
328C ARG* 2.9 40.9 - - + +
350C VAL* 1.3 75.6 - - - +
352C GLY* 1.3 55.7 + - - +
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Residues in contact with GLY 352 (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 LEU* 3.7 13.0 - - - -
154C SER 2.9 12.6 - - - -
155C LEU* 3.9 5.4 - - - -
238C LEU* 3.8 7.8 - - - +
326C ALA* 3.1 7.5 - - - +
327C PHE* 3.0 38.5 + - - +
351C GLN* 1.3 75.5 - - - +
353C GLN* 1.3 60.4 + - - -
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Residues in contact with GLN 353 (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 LEU* 3.4 5.3 - - - +
154C SER 2.8 35.1 + - - -
234C VAL 4.1 1.0 + - - -
235C ASP* 3.1 22.8 - - - +
236C ALA* 3.8 11.7 - - - +
237C HIS* 2.9 52.1 + - + +
238C LEU* 3.9 14.6 + - + +
325C VAL* 3.4 12.6 - - + +
326C ALA* 4.3 1.3 - - + +
352C GLY* 1.3 74.5 - - - +
354C VAL* 1.3 73.2 + - - +
355C HIS* 3.6 25.1 + - - +
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Residues in contact with VAL 354 (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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151C ASN* 3.8 25.4 - - + -
152C LEU 3.7 6.7 - - - +
153C LEU* 4.5 2.2 - - - +
237C HIS* 6.1 0.2 - - - -
264C LEU* 4.9 2.9 - - + -
283C GLY* 3.6 30.8 - - - +
284C VAL 4.0 5.6 - - - +
285C MET* 2.9 45.1 - - + +
325C VAL* 3.0 25.2 + - - +
353C GLN* 1.3 84.3 + - - +
355C HIS* 1.3 63.9 + - - +
356C PRO* 4.1 4.0 - - - +
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Residues in contact with HIS 355 (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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151C ASN* 3.4 4.2 - - - +
152C LEU* 2.8 39.3 + - + +
154C SER* 3.7 12.5 - - - -
164C PHE* 5.8 0.7 - + - -
233C PRO* 3.6 26.0 - - + +
234C VAL 3.2 26.5 - - - -
235C ASP* 2.5 25.3 + - - -
353C GLN* 3.6 24.3 + - - -
354C VAL* 1.3 75.5 - - - +
356C PRO* 1.3 73.0 - - + +
358C TYR* 3.8 26.8 - + + +
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Residues in contact with PRO 356 (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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6C MET* 4.5 3.5 - - - +
151C ASN* 3.4 8.3 - - - +
282C ALA* 3.8 12.1 - - + +
283C GLY* 3.4 22.9 - - - +
353C GLN* 6.3 0.2 - - - +
354C VAL 4.2 4.3 - - - +
355C HIS* 1.3 89.0 - - + +
357C ASN* 1.3 71.6 + - + +
358C TYR* 3.1 8.8 + - + +
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Residues in contact with ASN 357 (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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6C MET* 3.4 25.7 - - + +
149C PRO* 3.6 42.3 - - + +
150C MET* 3.5 8.6 + - - -
151C ASN* 3.1 10.9 + - - +
282C ALA* 3.4 32.0 + - + +
355C HIS 3.6 0.8 + - - -
356C PRO* 1.3 71.5 - - + +
358C TYR* 1.3 59.6 + - - +
359C PHE 3.6 1.3 - - - -
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Residues in contact with TYR 358 (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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6C MET* 3.9 31.0 + - + +
92C MET* 4.1 16.8 - - + -
97C TRP* 3.1 26.0 - - - -
101C ILE* 4.0 32.2 - - + +
102C GLN* 4.9 2.1 + - - -
150C MET 2.9 6.4 + - - +
152C LEU* 4.0 36.6 - - + -
233C PRO* 3.2 26.6 - - + +
355C HIS* 3.8 27.4 - - + +
356C PRO* 4.0 6.3 - - + +
357C ASN* 1.3 75.1 - - - +
359C PHE* 1.3 60.4 + - + +
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Residues in contact with PHE 359 (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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6C MET* 5.3 2.0 - - - +
84C MET* 5.6 0.4 - - - -
88C VAL* 4.6 2.7 - - + -
101C ILE* 3.4 32.8 - - + +
102C GLN* 5.5 0.4 - - - +
103C LYS 5.7 0.2 - - - +
105C LEU* 4.0 22.9 - - + -
149C PRO* 3.2 4.9 - - - +
150C MET* 2.8 41.0 + - + -
151C ASN 3.7 21.1 - - - -
152C LEU* 3.9 25.1 - - + -
166C VAL* 3.9 22.9 - - + -
265C HIS* 6.2 0.2 - - - -
357C ASN 3.6 0.8 - - - -
358C TYR* 1.3 78.8 - - - +
360C TRP* 1.3 77.7 + - - +
361C MET* 3.2 35.2 - - + -
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Residues in contact with TRP 360 (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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6C MET* 3.1 32.4 - - + +
7C GLY 3.5 22.9 - - - +
8C SER* 3.9 27.8 + - - -
9C GLY 4.1 13.5 - - - -
101C ILE 4.6 1.6 + - - -
102C GLN* 3.5 25.4 - - + +
103C LYS 4.3 2.1 + - - +
104C PRO* 3.9 18.0 - - + +
105C LEU* 3.1 20.0 + - - +
147C LEU* 3.6 31.0 - - + -
148C SER 3.6 15.9 - - - -
149C PRO* 3.6 30.1 - - + -
359C PHE* 1.3 86.9 - - - +
361C MET* 1.3 61.8 + - - +
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Residues in contact with MET 361 (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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84C MET* 4.4 14.6 - - + +
105C LEU* 3.2 23.3 - - + +
106C CYS* 4.2 2.9 - - - -
107C SER* 4.6 2.0 - - - -
116C LEU* 3.9 34.3 - - + -
120C LEU* 3.8 21.5 - - + -
147C LEU* 3.2 5.4 - - - -
148C SER 2.8 33.5 + - - +
150C MET* 3.7 23.1 - - + -
265C HIS* 5.6 0.4 - - - +
359C PHE* 3.2 35.8 + - + -
360C TRP* 1.3 72.3 - - - +
362C VAL* 1.3 70.0 + - - +
363C SER* 3.3 1.8 + - - -
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Residues in contact with VAL 362 (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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11C LEU* 4.4 6.7 - - + -
74C ALA* 5.3 3.1 - - + -
105C LEU 3.0 17.9 + - - +
106C CYS* 3.6 34.8 - - + -
107C SER 5.2 0.4 - - - +
120C LEU* 3.8 19.9 - - - +
138C CYS 4.9 1.3 - - - +
141C LEU* 4.3 8.0 - - + +
142C LEU* 4.0 36.1 - - + +
146C LEU 3.4 11.9 - - - +
147C LEU* 3.5 17.3 - - + -
361C MET* 1.3 75.1 - - - +
363C SER* 1.3 63.2 + - - +
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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