Contacts of the strand formed by residues 320 - 329 (chain A) in PDB entry 4F1Z
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A PHE* 3.8 8.5 - - - +
246A LYS* 5.7 1.6 - - + -
318A ASN 4.2 6.1 - - - +
319A ILE* 1.3 88.1 - - - +
321A GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 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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244A ASN* 3.9 5.9 - - - +
245A PHE* 3.4 43.8 + - - +
285A ILE* 5.5 3.1 - - - -
286A LYS 5.9 3.1 - - - -
320A ASN* 1.3 76.2 - - - +
322A GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 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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243A ALA 3.5 13.2 - - - +
244A ASN* 4.3 21.0 + - - +
245A PHE* 3.4 13.2 - - - -
285A ILE* 4.6 13.7 - - - +
321A GLY* 1.3 76.1 + - - +
323A PHE* 1.3 66.3 + - - +
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Residues in contact with PHE 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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221A ALA* 6.1 0.2 - - + -
241A MET* 3.7 34.3 - - + -
242A ALA* 3.6 3.1 - - - +
243A ALA* 3.4 42.6 + - + +
244A ASN 6.0 0.2 - - - -
245A PHE* 4.0 26.7 - + + -
257A PHE* 5.1 2.0 - + - -
285A ILE* 5.2 12.8 - - + -
307A PHE* 4.5 21.8 - + + -
322A GLN* 1.3 80.5 - - - +
324A SER* 1.3 67.1 + - - +
325A LEU* 3.5 25.6 - - + -
346A ILE* 3.3 39.3 - - + -
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Residues in contact with SER 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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240A PHE* 3.8 22.3 - - - +
241A MET 3.4 7.4 + - - -
242A ALA* 4.3 9.0 - - - +
323A PHE* 1.3 76.7 - - - +
325A LEU* 1.3 63.8 + - - +
326A PRO* 4.3 0.2 - - - -
530A TYR 5.6 0.2 + - - -
531A GLY* 2.9 33.9 - - - -
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Residues in contact with LEU 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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240A PHE* 3.3 4.0 - - - -
241A MET* 2.8 68.4 + - + +
280A MET* 6.0 1.6 - - + -
282A ILE* 4.4 20.0 - - + -
305A TYR* 3.8 32.1 - - + +
307A PHE* 4.0 14.4 - - + -
323A PHE* 3.5 24.5 - - + -
324A SER* 1.3 83.4 + - - +
326A PRO* 1.3 75.8 - - + +
327A LEU* 3.8 0.3 - - - +
531A GLY* 4.1 13.5 - - - -
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Residues in contact with PRO 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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239A THR 3.6 9.6 - - - +
240A PHE* 3.5 12.5 - - + -
267A GLY* 4.3 5.2 - - - +
305A TYR* 3.8 11.6 + - - -
324A SER 3.9 0.4 - - - +
325A LEU* 1.3 92.8 - - + +
327A LEU* 1.3 66.1 + - - +
328A PHE* 3.4 29.2 - - + -
529A ARG* 4.4 2.9 - - + -
530A TYR 3.3 29.2 - - - +
531A GLY* 3.3 20.4 - - - +
17Q SER* 4.1 12.8 - - - +
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Residues in contact with LEU 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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226A LEU* 3.7 19.7 - - + -
231A PHE* 4.4 1.5 - - - -
238A ASN* 3.3 5.7 - - - +
239A THR* 3.0 48.4 + - + +
241A MET* 3.7 35.4 - - + +
261A LEU* 4.1 26.0 - - + -
265A VAL* 4.3 17.3 - - + -
266A THR 3.6 14.1 - - - +
305A TYR* 4.4 2.0 - - - +
325A LEU 3.8 7.0 - - - +
326A PRO* 1.3 80.8 - - - +
328A PHE* 1.3 62.9 + - - +
344A ILE* 3.8 11.9 - - + -
355A ILE* 5.8 0.4 - - + -
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Residues in contact with PHE 328 (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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231A PHE* 4.9 3.1 - - - -
237A GLY 4.8 2.7 - - - +
238A ASN* 3.5 36.8 - - + +
265A VAL* 3.2 9.2 - - - +
266A THR* 2.9 27.4 + - - +
267A GLY 4.0 3.6 - - - -
268A ASN 3.9 5.8 - - - -
269A GLY* 3.4 34.3 - - - +
326A PRO* 3.4 34.3 - - + -
327A LEU* 1.3 75.7 - - - +
329A THR* 1.3 64.7 + - + +
357A TYR* 4.1 2.2 + - - -
529A ARG* 4.1 8.5 - - + -
15Q GLY* 3.6 15.7 - - - +
16Q GLY 3.3 33.4 - - - -
17Q SER* 3.7 17.3 - - - -
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Residues in contact with THR 329 (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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231A PHE* 4.5 6.1 - - - -
233A PRO* 3.7 31.6 - - + +
237A GLY 5.6 0.2 + - - -
264A SER 3.8 0.2 - - - -
266A THR* 3.3 14.6 + - - +
269A GLY* 4.6 3.9 - - - -
270A ASP* 6.3 0.2 - - - -
328A PHE* 1.3 83.0 - - + +
330A ASP* 1.3 66.3 + - - +
331A ARG* 3.8 29.9 + - + +
357A TYR* 3.5 29.3 + - - -
359A TYR* 2.7 24.8 + - - +
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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