Contacts of the helix formed by residues 314 - 326 (chain B) in PDB entry 6T2C
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 ASN 314 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B PRO* 3.4 23.4 - - + +
69B ILE* 3.4 28.6 - - + +
81B GLY 5.3 1.6 - - - +
312B ASN 3.3 7.4 + - - +
313B GLN* 1.3 71.8 - - - +
315B PRO* 1.3 75.0 - - - +
316B ARG* 3.2 35.4 + - - +
317B ILE* 3.3 20.8 + - + +
318B PHE* 3.2 14.4 - - - -
404B SER 3.8 1.2 - - - +
405B PRO* 3.3 24.3 - - - +
406B GLY 3.5 2.5 + - - +
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Residues in contact with PRO 315 (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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313B GLN 4.1 3.1 - - - +
314B ASN* 1.3 94.9 - - - +
316B ARG* 1.3 58.9 + - - +
318B PHE* 3.1 16.2 + - + +
319B LEU 2.9 21.8 + - - -
341B PRO* 3.5 29.0 - - + +
344B PHE* 3.8 22.4 - - + +
345B SER* 3.9 11.7 - - - +
347B LYS* 4.1 4.7 - - - +
404B SER 3.7 12.6 - - - +
406B GLY 4.3 4.0 - - - +
407B MET* 3.7 19.7 - - + -
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Residues in contact with ARG 316 (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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217A GLN 3.3 18.4 + - - -
218A SER* 3.4 14.0 - - - +
219A LEU 2.9 40.4 + - - +
220A PRO* 4.6 2.3 - - + +
229A PHE* 5.1 3.6 - - - -
65B GLN* 4.0 9.5 + - - +
66B LEU 3.9 9.5 + - - -
67B ASN* 3.1 37.5 + - - +
69B ILE* 3.7 17.2 - - + +
314B ASN* 3.2 19.9 - - - +
315B PRO* 1.3 73.0 - - - +
317B ILE* 1.3 61.2 + - - +
319B LEU* 3.2 10.3 + - - +
320B ALA* 3.0 27.4 + - - +
345B SER* 3.3 22.9 + - - +
404B SER* 3.1 25.3 + - - -
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Residues in contact with ILE 317 (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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69B ILE* 3.8 38.4 - - + -
83B ALA* 3.9 25.6 - - + +
85B THR* 4.5 9.6 - - - +
88B VAL* 3.8 35.2 - - + -
313B GLN* 6.1 1.1 - - + -
314B ASN* 3.3 18.6 + - + +
315B PRO 3.2 0.2 - - - -
316B ARG* 1.3 77.1 - - - +
318B PHE* 1.3 60.3 + - + +
320B ALA* 3.3 4.8 + - - +
321B MET* 2.9 35.3 + - - +
419B LEU* 4.6 12.6 - - + -
473B VAL 5.0 3.8 - - - +
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Residues in contact with PHE 318 (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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313B GLN* 3.4 43.5 - - + -
314B ASN 3.2 25.1 - - - -
315B PRO* 3.1 15.7 + - + +
317B ILE* 1.3 79.6 - - + +
319B LEU* 1.3 56.9 + - - +
321B MET* 3.6 14.6 - - - +
322B VAL* 2.9 34.1 + - - +
341B PRO* 4.1 10.3 - - + -
407B MET* 3.6 22.9 - - + -
412B PHE* 4.3 12.3 - + + -
415B LEU* 3.6 40.6 - - + -
416B SER* 3.7 16.2 - - - -
419B LEU* 5.3 6.1 - - + -
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Residues in contact with LEU 319 (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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218A SER* 3.3 25.4 - - - +
219A LEU* 4.0 15.9 - - + -
220A PRO* 6.0 0.2 - - + -
226A TYR* 4.7 4.0 - - + -
229A PHE* 4.4 8.1 - - + -
315B PRO 2.9 8.4 + - - +
316B ARG* 3.2 10.7 + - - +
318B PHE* 1.3 74.4 - - - +
320B ALA* 1.3 60.1 + - - +
322B VAL* 3.4 3.7 + - + +
323B LEU* 2.9 46.0 + - + +
338B ALA* 3.6 43.1 - - + +
341B PRO* 3.8 18.3 - - + +
342B ILE* 4.1 16.8 - - + -
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Residues in contact with ALA 320 (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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220A PRO* 5.9 0.2 - - + -
229A PHE* 3.9 25.9 - - + -
233A VAL* 4.7 0.7 - - - -
85B THR* 4.0 17.0 - - - +
88B VAL* 5.1 5.8 - - + -
89B LEU* 3.7 18.3 - - + +
316B ARG 3.0 12.7 + - - +
317B ILE* 3.3 9.8 + - - +
319B LEU* 1.3 76.1 - - - +
321B MET* 1.3 57.3 + - - +
323B LEU* 3.5 3.2 + - - +
324B ARG* 2.9 30.5 + - - +
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Residues in contact with MET 321 (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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88B VAL* 3.8 17.5 - - + -
89B LEU* 5.7 0.2 - - - -
92B ILE* 4.1 18.8 - - + -
317B ILE* 2.9 22.8 + - - +
318B PHE* 3.6 20.2 - - - +
319B LEU 3.2 0.2 - - - -
320B ALA* 1.3 77.3 - - - +
322B VAL* 1.3 60.9 + - + +
324B ARG* 3.2 4.5 + - - +
325B ILE* 2.9 38.3 + - + +
415B LEU* 3.6 37.7 - - + +
418B VAL* 3.8 21.1 - - + -
419B LEU* 4.0 28.3 - - - +
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Residues in contact with VAL 322 (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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255B VAL* 4.6 13.9 - - + -
258B LEU* 5.3 9.4 - - + -
318B PHE 2.9 23.6 + - - +
319B LEU* 3.4 20.9 - - + +
321B MET* 1.3 74.7 - - - +
323B LEU* 1.3 54.2 + - - +
325B ILE* 4.2 8.5 - - + -
326B THR* 2.5 34.8 + - + +
334B ARG 5.5 1.2 - - - +
337B LEU* 3.9 27.6 - - + +
338B ALA* 4.3 5.4 - - + -
341B PRO* 4.3 6.1 - - + -
415B LEU* 3.8 27.4 - - + -
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Residues in contact with LEU 323 (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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226A TYR* 4.0 29.4 - - + +
229A PHE* 4.0 28.7 - - + -
230A LYS* 4.0 28.5 - - + -
233A VAL* 3.6 18.1 - - + +
319B LEU* 2.9 32.3 + - + +
320B ALA* 4.0 1.3 - - - +
322B VAL* 1.3 81.7 - - - +
324B ARG* 1.3 61.7 + - - +
325B ILE 3.5 0.4 - - - -
326B THR* 3.9 1.8 - - - -
327B ALA* 3.8 4.7 + - - +
334B ARG* 2.7 43.9 + - + +
338B ALA* 4.3 8.3 - - + -
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Residues in contact with ARG 324 (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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233A VAL* 3.6 22.5 + - + +
234A SER 6.0 0.8 - - - -
236A PHE* 4.6 15.8 + - - +
89B LEU* 3.9 21.0 + - + +
92B ILE* 3.7 26.2 - - + -
93B GLU* 3.5 40.0 + - - +
96B ASP* 4.2 21.4 + - - +
103B PHE* 4.9 3.8 - - - -
320B ALA 2.9 18.8 + - - +
321B MET* 3.2 3.3 + - - +
323B LEU* 1.3 77.7 - - - +
325B ILE* 1.3 63.1 + - - +
327B ALA* 3.5 20.0 - - - +
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Residues in contact with ILE 325 (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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92B ILE* 4.1 9.4 - - + -
103B PHE* 3.8 43.7 - - + +
104B GLU* 5.0 2.3 - - - +
107B CYS* 4.1 13.3 - - - -
258B LEU* 4.1 19.5 - - + -
262B ILE* 3.8 33.2 - - + -
321B MET* 2.9 27.0 + - + +
322B VAL* 4.5 6.7 - - - -
324B ARG* 1.3 79.2 - - - +
326B THR* 1.3 57.8 + - + +
327B ALA* 3.2 6.9 + - - +
329B GLN* 5.1 0.3 - - - +
415B LEU* 4.7 14.1 - - + -
418B VAL* 4.6 16.6 - - + -
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Residues in contact with THR 326 (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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107B CYS* 3.7 20.0 - - - -
258B LEU* 4.4 7.4 - - + -
322B VAL 2.5 27.2 + - - +
323B LEU* 3.9 2.1 - - - -
324B ARG 3.4 0.2 - - - -
325B ILE* 1.3 75.6 - - + +
327B ALA* 1.3 61.7 + - - +
329B GLN* 3.4 26.6 + - - +
333B PHE* 3.8 17.3 - - + -
334B ARG* 3.1 37.4 + - - +
337B LEU* 4.1 16.8 - - + +
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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