Contacts of the strand formed by residues 199 - 207 (chain A) in PDB entry 5PJP
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 TYR 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ILE* 4.1 9.9 - - + -
39A GLU* 2.6 35.9 + - - -
194A GLU* 4.1 0.2 - - - -
198A LEU* 1.3 76.0 - - - +
200A SER* 1.3 60.3 + - - +
273A VAL* 4.3 2.2 - - + -
274A THR 3.2 17.0 - - - +
275A PHE* 3.5 16.8 - + - -
276A PRO* 3.5 27.1 - - + -
294A ASN* 3.0 19.4 + - - +
295A PHE* 3.1 61.3 + + + +
296A ALA* 4.2 3.1 - - - -
297A THR* 2.8 39.2 + - + +
299A ARG* 3.7 7.6 + - - +
300A TRP* 3.9 6.7 - - + -
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Residues in contact with SER 200 (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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194A GLU* 3.7 13.2 - - - -
199A TYR* 1.3 74.8 - - - +
201A ILE* 1.3 60.9 + - - +
202A ASN* 5.7 0.2 - - - +
273A VAL* 3.3 7.6 - - - +
274A THR* 2.7 55.8 + - - +
293A ILE 3.4 8.7 - - - -
294A ASN* 3.7 6.1 - - - -
295A PHE* 3.9 4.0 - - - -
404A OGA 2.8 29.2 + - - -
412A EDO 4.1 6.1 - - - -
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Residues in contact with ILE 201 (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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31A PHE* 3.6 30.1 - - + -
152A TRP* 3.7 20.2 - - + -
154A LEU* 3.6 24.4 - - + +
157A LEU* 4.2 3.6 - - + -
200A SER* 1.3 75.6 - - - +
202A ASN* 1.3 62.8 + - - +
203A TYR 4.3 0.2 - - - -
271A PHE* 3.7 20.2 - - + -
272A MET 3.3 10.8 - - - +
273A VAL* 3.9 7.9 - - + -
292A ALA* 3.0 24.2 - - - +
293A ILE* 3.0 28.2 + - + +
295A PHE* 3.8 17.3 - - + -
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Residues in contact with ASN 202 (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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181A TYR* 5.3 0.8 - - - -
200A SER* 5.7 0.4 - - - +
201A ILE* 1.3 74.4 - - - +
203A TYR* 1.3 60.3 + - - +
210A LYS* 4.2 2.4 - - - +
212A TRP* 3.8 22.9 - - + -
266A GLN* 3.2 20.3 + - - +
271A PHE* 3.3 6.7 - - - -
272A MET 2.8 39.3 + - - +
290A ALA* 3.7 18.2 - - - +
291A GLU 3.3 7.2 - - - -
292A ALA* 3.9 7.2 - - - +
404A OGA 3.1 49.2 + - - +
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Residues in contact with TYR 203 (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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57A TRP* 3.4 17.1 - + - -
59A ALA* 3.7 11.4 - - + -
63A TYR* 4.0 1.1 + - - -
145A PHE* 3.8 14.8 - + + -
154A LEU* 4.1 3.3 - - + +
202A ASN* 1.3 75.2 - - - +
204A LEU* 1.4 57.2 + - - +
205A HIS* 3.3 52.1 + + - -
269A GLY* 3.3 36.7 - - - -
270A GLU 3.7 7.2 - - - -
271A PHE* 3.6 35.2 - + + -
290A ALA* 3.2 3.3 - - - -
291A GLU* 2.8 41.3 + - + +
410A EDO 3.0 31.7 + - - -
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Residues in contact with LEU 204 (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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202A ASN* 4.9 0.2 - - - +
203A TYR* 1.4 70.9 - - - +
205A HIS* 1.3 61.6 + - - +
206A LEU 4.3 2.0 - - - +
208A GLU 3.6 17.0 - - - +
209A PRO* 4.1 1.3 - - + -
210A LYS* 4.1 9.6 - - + +
266A GLN* 3.5 45.4 - - + +
267A GLU* 3.6 20.4 - - - +
268A ALA* 3.5 9.3 - - + +
269A GLY* 2.8 31.5 + - - -
270A GLU 3.2 8.5 + - - +
288A ASN* 3.9 28.0 - - + +
289A CYS 3.6 19.3 - - - +
290A ALA* 4.0 9.2 - - + +
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Residues in contact with HIS 205 (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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59A ALA* 4.2 3.6 - - + -
63A TYR* 2.7 52.1 + + + -
144A LEU* 3.6 33.3 - - + +
145A PHE* 3.8 13.9 - + - -
180A LEU* 4.8 0.4 - - + -
203A TYR* 3.3 25.3 + + - -
204A LEU* 1.3 74.6 - - - +
206A LEU* 1.3 61.4 + - + +
268A ALA* 4.5 5.5 - - - +
269A GLY 4.7 1.9 + - - -
289A CYS* 2.8 19.6 + - - +
290A ALA 4.3 3.4 - - - -
291A GLU* 2.8 50.2 + - + +
410A EDO 5.4 0.5 + - - -
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Residues in contact with LEU 206 (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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63A TYR* 4.0 31.0 - - + +
66A ILE* 3.7 29.8 - - + -
102A ARG* 6.2 0.7 - - - +
204A LEU* 3.4 4.0 - - - +
205A HIS* 1.3 85.3 - - + +
207A GLY* 1.4 65.3 + - - +
268A ALA* 4.3 6.7 - - - +
287A PHE* 4.3 20.2 - - + -
288A ASN* 3.1 6.6 - - - +
289A CYS* 2.9 33.9 + - + +
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Residues in contact with GLY 207 (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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204A LEU* 5.6 0.2 - - - -
206A LEU* 1.4 82.2 - - - +
208A GLU* 1.3 76.2 + - - +
209A PRO* 4.6 0.7 - - - +
268A ALA* 3.8 20.6 + - - +
287A PHE* 3.4 12.6 - - - -
288A ASN* 4.2 0.4 - - - -
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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