Contacts of the strand formed by residues 302 - 316 (chain C) in PDB entry 2VDE
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 GLY 302 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A TYR* 3.3 34.6 + - - +
77A ARG* 3.9 1.0 - - - +
79A ALA* 3.6 10.7 - - - +
277C GLY 3.1 12.8 - - - -
278C ILE* 3.8 5.4 - - - -
279C SER* 4.4 1.8 - - - -
301C MET* 1.3 76.9 - - - +
303C GLN* 1.3 73.5 + - - +
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Residues in contact with GLN 303 (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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73A SER* 3.2 25.3 + - - +
74A ASN 3.7 12.1 - - - +
76A TYR* 3.3 12.1 - - - -
79A ALA* 4.3 8.3 - - - +
275C SER 5.4 0.2 - - - -
276C THR* 3.3 0.5 - - - -
277C GLY* 2.5 40.4 + - - +
302C GLY* 1.3 85.0 - - - +
304C ASN* 1.3 73.3 + - - +
305C LYS* 3.6 31.3 - - + +
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Residues in contact with ASN 304 (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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72A TYR* 3.2 8.0 - - + +
73A SER 3.5 0.2 - - - -
74A ASN* 2.8 60.8 + - + +
76A TYR* 3.0 26.4 + - + -
275C SER 3.6 3.8 - - - -
276C THR* 3.4 11.5 - - - -
303C GLN* 1.3 81.5 - - - +
305C LYS* 1.3 61.6 + - - +
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Residues in contact with LYS 305 (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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71A THR* 4.2 19.5 - - + -
72A TYR* 3.2 6.1 - - - +
73A SER* 3.9 18.4 - - - +
274C ALA* 3.4 0.8 - - - +
275C SER* 2.9 50.0 + - - +
303C GLN* 3.6 33.9 - - + +
304C ASN* 1.3 75.6 - - - +
306C VAL* 1.3 70.3 + - - +
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Residues in contact with VAL 306 (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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70A TYR* 3.9 7.3 - - + +
71A THR* 3.5 3.2 - - - -
72A TYR* 2.8 46.7 + - + +
272C LEU* 5.3 10.5 - - + -
273C THR 3.5 8.1 - - - +
274C ALA* 4.0 14.1 - - + -
305C LYS* 1.3 80.3 - - - +
307C GLY* 1.3 63.5 + - - +
308C LEU* 6.3 0.4 - - + -
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Residues in contact with GLY 307 (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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70A TYR* 2.9 13.9 - - - -
71A THR* 4.2 7.2 - - - +
272C LEU* 3.5 2.9 - - - +
273C THR* 2.7 44.2 + - - +
306C VAL* 1.3 77.3 - - - +
308C LEU* 1.3 70.5 + - - +
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Residues in contact with LEU 308 (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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68A ALA 3.8 0.9 - - - +
69A ASP* 3.2 7.9 - - - +
70A TYR* 2.7 50.9 + - + +
97C ILE* 5.4 1.1 - - + -
270C LEU* 4.3 27.4 - - + -
271C ASP 3.5 9.4 - - - +
272C LEU* 3.8 27.1 - - + -
306C VAL* 6.3 0.7 - - + -
307C GLY* 1.3 81.4 - - - +
309C SER* 1.3 60.4 + - - +
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Residues in contact with SER 309 (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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68A ALA 3.6 3.2 + - - -
69A ASP* 3.7 16.8 + - - -
269C THR 3.9 0.2 - - - +
270C LEU* 3.4 7.7 - - - +
271C ASP* 2.8 52.3 + - - +
273C THR* 5.2 7.8 + - - -
308C LEU* 1.3 74.0 - - - +
310C PHE* 1.3 64.1 + - - +
311C SER* 6.0 0.2 - - - -
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Residues in contact with PHE 310 (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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66A LEU* 4.6 14.4 - - + -
67A GLY* 3.3 8.1 - - - -
68A ALA* 2.8 57.4 + - + +
268C PRO* 4.0 29.4 - - + -
269C THR 3.4 13.7 - - - -
270C LEU* 3.8 20.0 - - + -
309C SER* 1.3 78.3 + - - +
311C SER* 1.3 61.8 + - - +
312C LEU* 3.8 23.6 - - + -
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Residues in contact with SER 311 (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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66A LEU 3.8 5.7 + - - -
67A GLY* 4.8 0.6 - - - -
268C PRO* 3.3 5.2 - - - +
269C THR* 2.8 56.0 + - - +
309C SER* 4.4 0.6 - - - -
310C PHE* 1.3 76.1 - - - +
312C LEU* 1.3 63.5 + - - +
313C PRO* 4.4 2.6 - - - +
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Residues in contact with LEU 312 (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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65A GLY* 3.8 0.9 - - - -
66A LEU* 2.8 48.5 + - + +
266C HIS 3.8 11.0 - - - +
268C PRO* 3.8 22.4 - - + -
310C PHE* 3.8 21.5 - - + -
311C SER* 1.3 77.1 + - - +
313C PRO* 1.3 89.8 - - + +
314C ILE* 3.7 23.3 - - + -
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Residues in contact with PRO 313 (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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64A LEU 4.2 5.6 - - - +
65A GLY* 4.5 3.1 - - - -
265C GLY 3.8 20.4 - - - +
266C HIS* 3.6 21.0 - - - +
267C LEU 4.1 9.2 - - - +
311C SER* 4.4 3.1 - - - +
312C LEU* 1.3 96.0 - - + +
314C ILE* 1.3 63.7 + - - +
316C GLN* 3.8 26.9 - - + +
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Residues in contact with ILE 314 (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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64A LEU* 3.1 29.2 + - + +
65A GLY* 4.4 3.4 - - - +
66A LEU* 4.1 30.3 - - + +
91A LEU* 5.6 6.5 - - + -
312C LEU* 3.6 21.9 + - + -
313C PRO* 1.3 76.0 - - - +
315C TYR* 1.3 67.7 + - + +
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Residues in contact with TYR 315 (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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61A LEU* 3.4 25.8 - - - +
62A PRO* 3.5 34.1 - - + -
63A GLN* 3.4 1.6 - - - -
64A LEU* 2.7 50.9 + - + +
313C PRO 3.8 0.6 - - - -
314C ILE* 1.3 90.3 - - + +
316C GLN* 1.3 64.4 + - - +
317C GLY* 3.6 12.5 - - - -
318C GLY* 3.9 16.6 - - - -
321C ASN* 6.2 0.7 - - - -
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Residues in contact with GLN 316 (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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62A PRO 3.8 4.3 - - - -
63A GLN* 3.2 28.7 - - + +
64A LEU 5.4 1.1 - - - +
265C GLY 4.0 5.1 + - - -
313C PRO* 3.8 27.3 - - + +
315C TYR* 1.3 80.3 - - - +
317C GLY* 1.3 51.0 + - - +
318C GLY 2.7 16.8 + - - -
319C MET* 2.7 34.9 + - + +
320C VAL* 3.5 26.6 - - + +
1453C CL 3.9 12.2 - - + +
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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