Contacts of the strand formed by residues 397 - 406 (chain C) in PDB entry 2GVG
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 CYS 397 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C PHE* 3.5 15.5 - - + -
38C GLU 3.5 7.6 - - - -
39C CYS* 3.8 21.5 - - - +
40C ARG* 5.6 0.3 + - - -
153C VAL* 4.7 0.5 - - - +
156C TRP* 3.4 40.2 - - + -
159C ILE* 5.0 1.3 - - - -
160C THR* 4.1 9.2 - - - -
392C ARG* 2.7 47.4 + - + +
395C LEU* 3.9 15.5 - - - -
396C ASN* 1.3 73.0 - - - +
398C SER* 1.3 52.5 + - - +
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Residues in contact with SER 398 (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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36C TYR* 3.7 1.2 - - - +
37C PHE* 3.3 9.3 - - - -
38C GLU* 3.0 37.3 + - - +
40C ARG* 4.1 22.9 - - - -
153C VAL* 5.5 0.7 - - - -
392C ARG* 4.1 3.8 - - - +
396C ASN 3.2 7.4 + - - -
397C CYS* 1.3 75.2 - - - +
399C PHE* 1.3 61.8 + - - +
400C LYS* 3.4 20.0 + - - +
602C PO4 3.0 27.0 + - - -
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Residues in contact with PHE 399 (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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35C SER* 3.4 31.4 - - - -
36C TYR 3.3 15.9 - - - -
37C PHE* 4.3 9.9 - + + -
132C PHE* 4.2 11.0 - + - -
134C VAL* 4.1 25.6 - - + -
145C THR 4.1 13.0 - - - -
146C ASN* 3.5 16.1 + - - -
149C GLU* 3.0 62.5 + - + +
152C LEU* 4.4 7.9 - - + -
153C VAL* 3.4 22.0 - - + +
398C SER* 1.3 75.8 + - - +
400C LYS* 1.3 69.5 + - - +
602C PO4 4.3 3.7 + - - -
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Residues in contact with LYS 400 (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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247A HIS* 6.5 0.7 - - + -
35C SER* 3.1 6.6 - - - -
36C TYR* 2.7 61.6 + - + +
38C GLU* 5.0 2.4 + - + +
40C ARG* 3.6 19.9 - - - +
146C ASN* 5.8 0.9 - - - +
398C SER* 3.4 23.5 - - - +
399C PHE* 1.3 84.1 - - - +
401C CYS* 1.3 62.3 + - - +
415C LYS* 3.7 19.0 - - + +
423C LYS* 2.9 34.4 + - - +
424C ARG 4.0 1.8 + - - -
425C SER* 3.1 28.9 - - - +
602C PO4 4.3 7.4 - - - +
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Residues in contact with CYS 401 (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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248A SER* 3.5 37.8 - - - -
251A THR* 4.7 3.8 + - - +
252A ALA* 5.3 0.4 - - - -
26C TYR* 5.7 0.4 - - - -
33C VAL* 4.1 12.3 - - + -
34C TYR 3.8 7.2 - - - -
35C SER* 3.4 14.1 + - - +
146C ASN* 4.9 1.2 - - - +
400C LYS* 1.3 76.7 - - - +
402C SER* 1.3 61.0 + - - +
404C VAL* 3.3 33.9 - - - -
413C VAL* 3.4 24.1 - - + +
414C PHE* 4.3 5.9 - - - -
425C SER* 4.7 0.9 + - - -
426C LYS 4.7 0.9 - - - +
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Residues in contact with SER 402 (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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34C TYR* 3.0 20.9 + - - -
36C TYR* 3.9 21.2 - - - -
400C LYS 3.6 1.2 + - - -
401C CYS* 1.3 74.1 - - - +
403C TYR* 1.3 59.0 + - - +
413C VAL* 2.8 26.9 + - - -
426C LYS 3.3 18.8 - - - -
428C GLY* 2.6 45.5 + - - -
430C LEU* 4.3 2.2 - - - +
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Residues in contact with TYR 403 (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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32C LYS* 4.0 16.8 + - - -
34C TYR* 2.7 55.5 + + + +
402C SER* 1.3 82.3 + - - +
404C VAL* 1.3 64.6 + - - +
405C VAL* 3.9 16.8 - - + +
410C GLY* 3.5 39.8 + - - -
411C ILE 3.6 13.0 - - - -
412C ASN* 3.6 17.7 - - - -
413C VAL* 3.8 1.4 - - - +
428C GLY* 4.1 1.6 - - - -
429C ARG* 3.4 48.9 - - + +
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Residues in contact with VAL 404 (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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252A ALA* 4.3 23.1 - - + +
26C TYR* 5.7 0.2 - - + -
30C THR* 3.8 13.0 - - + +
32C LYS 3.2 16.4 - - - +
33C VAL* 4.4 7.2 - - + -
401C CYS* 3.3 24.5 - - - -
403C TYR* 1.3 83.0 - - - +
405C VAL* 1.3 68.1 + - - +
406C THR* 3.6 20.4 - - - +
409C LEU 3.9 0.5 - - - +
410C GLY* 3.0 3.6 - - - -
411C ILE* 2.9 38.6 + - + +
413C VAL* 4.2 12.3 - - + +
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Residues in contact with VAL 405 (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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29C ASN 3.9 0.2 - - - +
30C THR* 3.3 3.5 - - - +
31C SER* 2.8 50.7 + - - +
32C LYS* 3.2 38.2 + - + +
403C TYR* 3.9 10.5 - - + +
404C VAL* 1.3 81.9 - - - +
406C THR* 1.3 61.1 + - - +
408C GLY* 3.9 28.5 - - - +
409C LEU 3.5 4.9 - - - +
410C GLY* 3.8 11.2 - - - -
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Residues in contact with THR 406 (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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252A ALA 4.5 4.9 + - - -
27C PRO* 4.2 14.9 - - + +
28C PRO 3.0 28.7 - - - +
29C ASN 3.4 4.3 - - - +
30C THR* 3.2 17.0 + - - +
404C VAL* 3.6 12.2 - - - +
405C VAL* 1.3 73.2 - - - +
407C ASN* 1.3 87.3 + - - +
408C GLY 3.1 1.8 - - - -
409C LEU* 2.9 21.7 + - - +
411C ILE* 5.4 7.2 - - - +
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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