Contacts of the strand formed by residues 339 - 348 (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 PRO 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B PHE* 5.6 0.4 - - + -
332B VAL* 3.9 22.4 - - + -
337B ARG 4.3 0.7 - - - +
338B LYS* 1.4 87.1 - - + +
340B HIS* 1.3 59.9 + - - +
341B THR 4.0 0.4 - - - +
364B ILE* 3.3 20.7 - - + +
369B ILE* 3.5 16.0 - - + +
371B LYS* 4.8 9.6 - - - +
410B PHE* 3.6 50.5 - - + -
411B CYS 3.8 3.6 - - - +
413B LEU* 3.7 18.8 - - + -
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Residues in contact with HIS 340 (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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338B LYS* 3.4 17.2 + - + -
339B PRO* 1.3 74.3 - - - +
341B THR* 1.3 63.6 + - - +
363B PRO* 3.4 7.4 - - - +
364B ILE* 3.0 24.1 + - - +
369B ILE* 3.6 37.8 - - + +
412B ASN* 2.8 32.0 + - - +
414B LYS* 3.5 46.8 + - + +
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Residues in contact with THR 341 (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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339B PRO* 3.5 0.4 - - - +
340B HIS* 1.3 78.5 - - - +
342B VAL* 1.3 71.3 + - - +
361B GLN* 4.2 10.1 + - - +
362B CYS 3.2 18.6 + - - -
363B PRO* 4.3 2.0 - - + -
364B ILE* 3.9 5.7 - - - +
410B PHE* 3.6 4.7 - - - -
411B CYS* 3.1 42.4 + - - +
412B ASN* 3.1 37.0 - - + +
865P G 5.8 1.8 - - - -
866P T 4.4 15.3 + - - +
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Residues in contact with VAL 342 (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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341B THR* 1.3 75.8 + - - +
343B ARG* 1.3 64.2 + - - +
361B GLN* 3.1 3.5 - - - +
362B CYS* 3.0 31.1 + - - +
364B ILE* 3.1 33.7 - - + -
383B MSE 3.3 34.3 - - + -
386B ILE* 5.3 7.4 - - + -
387B LEU* 3.7 22.2 - - + -
390B LEU* 4.0 6.9 - - + +
408B VAL* 3.9 10.3 - - + -
409B CYS 3.4 11.2 - - - +
410B PHE* 3.6 7.6 - - + -
411B CYS* 5.5 0.2 - - - -
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Residues in contact with ARG 343 (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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342B VAL* 1.3 77.8 - - - +
344B LEU* 1.3 62.5 + - - +
345B ILE* 3.8 28.7 - - + +
359B SER* 3.7 21.6 + - - -
360B ARG 3.4 10.5 - - - +
361B GLN* 2.7 36.3 + - + +
387B LEU* 4.6 0.2 - - - -
407B SER 4.0 0.2 - - - +
408B VAL* 3.6 6.6 - - - +
409B CYS* 2.8 50.5 + - + +
411B CYS* 4.9 9.0 - - - -
867P G 3.6 20.1 + - - -
868P G 4.8 10.5 + - - -
869P A 6.1 1.0 - - - +
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Residues in contact with LEU 344 (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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321B ILE* 3.9 25.6 - - + -
343B ARG* 1.3 71.9 - - - +
345B ILE* 1.3 65.8 + - - +
346B ILE* 4.7 2.0 - - + -
359B SER* 3.1 23.9 - - - -
360B ARG 2.8 15.8 + - - +
387B LEU* 3.6 21.1 - - + +
390B LEU* 4.1 8.1 - - + +
391B PHE* 3.6 51.6 - - + +
394B MSE 3.7 15.1 - - + +
406B LEU* 4.4 8.3 - - + -
407B SER 3.5 18.8 - - - +
408B VAL* 4.3 8.1 - - + -
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Residues in contact with ILE 345 (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* 5.3 1.3 - - - -
343B ARG* 3.8 29.8 - - + +
344B LEU* 1.3 79.1 - - - +
346B ILE* 1.3 68.9 + - - +
357B ARG* 3.8 40.6 - - + +
358B GLU 3.3 11.9 - - - +
359B SER* 3.9 5.8 - - - -
405B LEU* 4.8 1.6 - - + -
406B LEU* 3.4 6.9 - - - +
407B SER* 2.7 55.6 + - - +
409B CYS* 3.9 20.9 - - + -
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Residues in contact with ILE 346 (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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344B LEU* 4.7 1.8 - - + -
345B ILE* 1.3 80.4 - - - +
347B ARG* 1.3 62.7 + - - +
348B ARG* 3.8 38.6 - - + +
357B ARG* 3.2 28.1 - - - +
358B GLU* 2.8 23.6 + - + +
391B PHE* 4.6 8.7 - - + -
394B MSE 4.0 28.3 - - + -
395B VAL* 3.8 18.2 - - + -
403B LEU* 4.1 15.5 - - + -
405B LEU* 3.5 8.7 - - - +
406B LEU* 3.8 19.5 - - + -
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Residues in contact with ARG 347 (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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307B SER* 3.7 5.9 - - - -
308B PHE 4.9 1.2 + - - +
346B ILE* 1.3 75.5 - - - +
348B ARG* 1.3 67.1 + - - +
356B GLY* 4.1 19.5 - - - +
357B ARG* 4.3 16.0 - - + +
403B LEU* 3.2 6.7 - - - +
404B THR* 2.6 74.0 + - + +
405B LEU* 3.1 31.1 + - + +
839T T 3.2 32.3 + - - -
840T T 2.7 40.4 + - - +
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Residues in contact with ARG 348 (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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346B ILE* 3.8 19.3 - - + +
347B ARG* 1.3 87.9 - - - +
349B TYR* 1.3 68.3 + - - +
350B SER 3.6 7.3 + - - +
356B GLY 4.7 4.4 + - - +
358B GLU* 2.8 48.3 + - - +
394B MSE 3.3 24.7 + - - -
395B VAL* 3.8 22.6 - - - +
396B ASN 4.6 2.4 - - - +
401B PHE* 5.0 7.7 - - - +
402B HIS 3.6 9.0 - - - +
403B LEU* 4.3 7.1 - - + +
404B THR* 4.4 1.9 - - - +
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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