Contacts of the strand formed by residues 316 - 327 (chain A) in PDB entry 2A73
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 MET 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A SER* 5.5 0.2 + - - -
210A PHE* 4.4 1.2 - - - -
307A THR* 3.6 32.3 - - + -
308A VAL 3.3 9.4 - - - +
309A ILE* 3.9 13.2 - - + -
314A SER 3.8 8.1 - - - +
315A ASP* 1.3 76.8 - - - +
317A VAL* 1.3 67.5 + - - +
318A GLN* 3.6 25.8 - - + +
733B ILE* 5.2 13.9 - - + -
734B ILE 4.5 9.9 - - - +
739B ILE* 5.1 6.5 - - + -
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Residues in contact with VAL 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PRO* 3.8 18.4 - - + -
209A SER* 4.4 2.9 - - - +
210A PHE* 3.3 54.3 - - + +
211A GLU* 5.0 0.4 - - - -
212A VAL* 3.7 21.1 - - + +
306A ALA 3.7 0.9 - - - +
307A THR* 3.7 1.7 - - - -
308A VAL* 3.0 33.1 + - - +
316A MET* 1.3 78.8 - - - +
318A GLN* 1.3 76.3 + - - +
741B SER* 4.4 11.4 - - - +
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Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A SER* 6.0 1.6 + - - -
306A ALA 3.2 4.7 - - - +
307A THR* 3.2 22.9 + - + +
316A MET* 3.6 19.5 - - + +
317A VAL* 1.3 87.1 - - - +
319A ALA* 1.3 63.9 + - - +
734B ILE 4.5 0.9 - - - +
735B ALA 3.1 29.4 + - - +
736B GLU* 4.0 9.7 - - - +
737B GLU* 4.4 2.2 - - - +
738B ASN 4.7 0.6 - - - +
739B ILE* 3.4 62.3 - - + +
741B SER* 4.1 12.7 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 3.3 45.1 - - + +
214A VAL* 3.5 16.0 - - + +
305A SER* 3.6 2.3 - - - -
306A ALA 2.8 36.5 + - - +
318A GLN* 1.3 78.5 - - - +
320A GLU* 1.3 60.8 + - - +
739B ILE 5.3 1.6 - - - -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 4.1 2.7 - - - -
259A ARG* 2.7 41.6 + - - -
303A TYR* 5.1 4.3 - - + -
304A VAL 3.4 15.0 - - - +
305A SER* 3.3 17.4 + - - +
319A ALA* 1.3 75.5 - - - +
321A ARG* 1.3 61.1 + - - +
322A SER* 3.9 12.9 + - - +
738B ASN* 3.4 30.9 + - - +
739B ILE 5.7 3.8 + - - +
740B VAL* 5.8 8.4 - - + +
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 2.8 35.6 + - + +
215A GLU* 3.2 27.3 - - - +
216A PRO* 3.5 33.2 + - + +
219A LYS* 5.2 14.8 - - - +
303A TYR* 3.4 1.9 - - - -
304A VAL* 2.9 34.6 + - + +
320A GLU* 1.3 70.8 - - - +
322A SER* 1.3 71.3 + - - +
324A ILE* 4.0 14.3 - - + +
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLN* 4.3 3.6 - - - -
259A ARG* 3.3 30.5 + - - -
302A LEU 3.8 1.6 - - - -
303A TYR* 3.4 18.2 - - - -
320A GLU* 3.9 10.7 + - - +
321A ARG* 1.3 84.9 - - - +
323A GLY* 1.3 66.0 + - - +
324A ILE* 3.2 3.6 + - - +
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Residues in contact with GLY 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLN* 4.3 7.3 + - - -
301A SER* 4.0 16.1 - - - -
302A LEU 3.3 4.9 + - - -
322A SER* 1.3 78.7 - - - +
324A ILE* 1.3 59.8 + - - +
325A PRO* 3.0 19.2 - - - +
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Residues in contact with ILE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO* 4.0 24.0 - - + -
219A LYS 4.1 4.7 - - - +
220A PHE* 4.1 23.3 - - - +
221A TYR 4.4 1.6 - - - +
229A LEU* 4.1 27.4 - - + -
301A SER* 3.2 1.8 - - - -
302A LEU* 2.7 49.6 + - + +
304A VAL* 4.0 17.9 - - + -
321A ARG* 4.0 30.3 - - + +
322A SER 4.5 1.6 - - - +
323A GLY* 1.3 73.8 - - - +
325A PRO* 1.3 72.9 - - + +
326A ILE* 3.4 1.0 + - - +
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Residues in contact with PRO 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LYS 3.2 22.9 - - - +
220A PHE* 3.4 7.8 - - - +
221A TYR 3.2 22.3 + - - -
300A LYS 4.1 4.3 - - - +
301A SER* 4.5 3.8 - - - -
323A GLY 3.0 12.3 - - - +
324A ILE* 1.3 82.5 - - - +
326A ILE* 1.3 61.4 + - - +
327A VAL* 4.1 5.6 - - + +
357A PRO* 4.0 39.9 - - + +
358A ASP* 4.8 6.7 - - + +
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 3.7 12.3 - - + +
223A ILE* 3.4 31.6 - - + -
253A ILE* 4.4 6.7 - - + -
285A LEU* 5.4 4.7 - - + -
297A LEU* 3.3 37.5 - - + +
298A VAL* 3.9 3.1 - - - +
299A GLY* 3.2 22.0 + - - -
300A LYS* 2.9 32.6 + - + +
301A SER 4.4 0.4 - - - +
302A LEU* 3.8 40.4 - - + -
324A ILE 3.4 1.1 + - - +
325A PRO* 1.3 71.7 - - - +
327A VAL* 1.3 65.5 + - - +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.8 32.5 - - + -
221A TYR 3.2 20.0 + - - +
222A TYR* 3.8 4.8 - - + +
223A ILE* 3.5 19.0 + - - +
298A VAL* 4.3 5.6 - - - -
325A PRO* 4.4 6.3 - - + +
326A ILE* 1.3 80.3 - - - +
328A THR* 1.3 60.7 + - - +
329A SER 3.3 26.9 - - - +
332A GLN* 5.8 4.7 - - + +
357A PRO* 3.9 25.1 - - + -
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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