Contacts of the strand formed by residues 302 - 311 (chain B) in PDB entry 3GV5
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 PHE 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PRO* 4.3 14.4 - - + -
301B SER* 1.3 78.6 - - - +
303B SER* 1.3 60.7 + - - +
328B LEU* 3.6 16.1 - - + +
331B ARG* 3.8 27.8 - - + +
332B VAL* 3.7 40.8 - - + -
335B ASP* 3.6 33.7 - - + -
337B ARG* 3.7 20.9 - - - -
339B PRO* 5.6 1.1 - - + -
409B CYS* 3.3 2.9 - - - -
410B PHE* 2.8 45.6 + + + +
413B LEU* 3.9 21.1 - - + -
843T C 3.5 4.9 - - - -
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B SER* 6.0 0.2 - - - -
302B PHE* 1.3 75.9 - - - +
304B GLU* 1.3 62.0 + - - +
305B GLU* 5.0 1.7 + - - -
328B LEU* 3.9 1.8 - - - -
331B ARG* 2.6 27.8 + - - -
345B ILE* 5.3 1.1 - - - -
407B SER* 3.9 11.7 + - - -
408B VAL 3.1 13.7 - - - -
409B CYS* 3.7 16.6 - - - -
842T T 3.3 30.5 - - - +
843T C 2.7 18.6 + - - -
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 3.9 7.7 + - - -
303B SER* 1.3 75.3 - - - +
305B GLU* 1.3 60.4 + - - +
324B LEU* 3.8 32.8 - - + +
327B SER* 3.7 24.3 + - - +
328B LEU* 3.6 21.8 - - + +
331B ARG* 2.8 30.0 + - - +
407B SER* 3.0 21.4 + - - -
408B VAL 2.9 12.6 + - - +
422B GOL 3.6 14.9 + - - -
842T T 3.7 12.0 + - - -
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B SER* 5.0 1.2 + - - -
304B GLU* 1.3 74.1 - - - +
306B ASP* 1.3 59.7 + - - +
324B LEU* 3.9 3.6 - - - -
357B ARG* 2.6 32.9 + - - -
405B LEU* 3.5 21.5 - - + +
406B LEU 3.3 11.9 - - - +
407B SER* 3.3 14.8 + - - +
422B GOL 2.6 35.9 + - - -
841T C 3.3 49.0 + - + +
842T T 3.0 26.3 + - - +
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 3.0 23.5 + - - -
97B GLU* 4.9 0.5 - - - +
305B GLU* 1.3 76.6 - - - +
307B SER* 1.3 65.4 + - - +
308B PHE* 3.4 21.1 - - + +
320B LYS* 5.1 7.8 + - + +
323B GLU* 5.0 8.6 - - - +
324B LEU* 4.3 14.1 - - + +
405B LEU* 3.4 6.0 - - - +
406B LEU 3.0 30.4 + - - +
422B GOL 2.9 22.4 + - - -
841T C 4.1 1.8 - - - -
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LYS* 3.0 40.0 + - - +
306B ASP* 1.3 77.6 + - - +
308B PHE* 1.3 64.4 + - - +
347B ARG* 3.7 6.5 - - - -
404B THR 3.3 12.6 - - - -
405B LEU* 4.2 6.7 - - - +
840T T 3.2 31.3 + - - -
841T C 2.8 23.4 + - - -
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LYS* 5.2 1.8 - - - +
306B ASP* 3.4 33.7 - - + +
307B SER* 1.3 80.4 - - - +
309B LYS* 1.3 66.3 + - - +
310B LYS 4.4 3.8 - - - +
311B CYS* 3.4 31.6 - - + -
320B LYS* 4.2 22.9 - - + +
347B ARG* 5.0 0.9 + - - -
403B LEU* 3.5 19.3 - - + -
404B THR* 3.0 25.2 + - - +
405B LEU 3.6 11.0 - - - -
406B LEU* 3.6 43.7 - - + -
840T T 5.2 0.4 + - - -
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B TYR* 6.1 7.5 - - - -
308B PHE* 1.3 75.2 - - - +
310B LYS* 1.3 54.3 + - + +
349B TYR* 4.9 1.7 - - - -
402B HIS* 2.8 26.9 - - - -
403B LEU 4.3 0.2 - - - -
404B THR* 3.6 9.3 + - - -
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Residues in contact with LYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B PHE* 3.4 9.1 - - - +
309B LYS* 1.3 81.5 - - + +
311B CYS* 1.3 53.2 + - - +
312B SER* 3.4 34.4 + - - +
316B GLU* 4.0 12.2 + - - +
320B LYS* 5.3 2.3 + - - -
402B HIS* 3.5 29.6 - - + +
403B LEU 3.5 7.2 - - - -
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Residues in contact with CYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B PHE* 3.4 24.9 - - + -
310B LYS* 1.3 66.6 - - - +
312B SER* 1.3 61.6 + - - +
313B SER 3.8 2.7 - - - -
316B GLU* 3.5 37.2 + - - -
317B ALA* 3.5 29.4 - - - -
320B LYS* 4.7 6.7 - - - +
401B PHE* 3.8 3.8 - - - -
402B HIS* 3.2 3.3 + - - -
403B LEU* 2.7 44.3 + - + +
406B LEU* 4.7 3.4 - - - -
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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