Contacts of the strand formed by residues 217 - 222 (chain A) in PDB entry 1PJQ
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 GLU 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ARG* 4.6 6.0 + - - +
177A ARG* 4.2 16.2 + - - +
216A GLY* 1.3 77.8 - - - +
218A VAL* 1.3 62.1 + - - +
219A VAL* 3.4 22.9 - - + +
238A GLN* 5.0 0.5 - - - +
290A ALA* 4.3 3.1 - - - +
294A LYS 3.1 5.9 + - - +
295A ARG* 3.9 34.0 + - + +
296A VAL* 2.7 36.2 + - - +
322A ILE* 4.3 3.8 - - - -
323A PRO* 3.3 24.6 - - + +
324A PHE* 5.5 1.7 - - - -
325A SER* 4.6 4.5 + - - -
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Residues in contact with VAL 218 (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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217A GLU* 1.3 78.0 - - - +
219A VAL* 1.3 68.4 + - - +
220A LEU* 4.9 0.4 - - + +
286A LEU* 4.0 41.5 - - + +
290A ALA* 3.9 19.5 - - + -
296A VAL* 3.3 10.3 - - + +
298A ARG* 5.0 4.7 - - + -
314A LEU* 3.9 20.1 - - + +
317A LEU* 3.8 24.2 - - + -
322A ILE* 4.5 2.9 - - + -
323A PRO 3.1 4.8 + - - -
324A PHE* 3.0 26.5 - - - +
325A SER 3.3 2.1 + - - +
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 3.4 30.7 - - + +
218A VAL* 1.3 79.8 - - - +
220A LEU* 1.3 64.9 + - - +
221A VAL* 3.6 18.2 + - + -
238A GLN* 3.6 31.0 - - + +
295A ARG* 5.4 2.9 - - + -
296A VAL 2.7 14.8 + - - +
297A VAL* 3.4 11.1 - - + +
298A ARG 3.0 22.7 + - - -
325A SER* 3.4 24.9 - - - +
327A VAL* 4.2 6.5 - - + -
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Residues in contact with LEU 220 (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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218A VAL* 4.1 1.9 - - + -
219A VAL* 1.3 72.5 - - - +
221A VAL* 1.3 57.0 + - - +
286A LEU* 5.6 0.2 - - + -
298A ARG* 3.5 35.7 - - + +
300A LYS* 4.5 10.8 - - + -
304A PRO* 4.3 12.1 - - + -
305A PHE* 4.0 11.0 - - + -
310A GLY* 3.6 27.4 - - - +
313A GLU* 4.2 8.1 - - + +
314A LEU* 3.3 41.3 - - + -
325A SER 3.0 11.4 + - - +
326A VAL* 3.5 9.6 - - + -
327A VAL 2.7 32.8 + - - +
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Residues in contact with VAL 221 (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 VAL* 3.6 16.8 + - + -
220A LEU* 1.3 79.6 - - - +
222A GLY* 1.3 72.6 + - - +
223A ALA 3.4 0.5 + - - -
231A LEU* 4.6 2.2 - - + -
235A GLY* 3.9 26.0 - - - +
238A GLN* 4.0 15.7 - - + -
239A ILE* 4.7 3.1 - - + -
297A VAL* 3.8 26.2 - - + -
298A ARG 3.0 8.1 + - - +
299A LEU* 3.7 13.8 - - + +
300A LYS* 3.1 26.7 + - - +
304A PRO* 4.5 4.6 - - - +
327A VAL* 3.7 11.4 - - + -
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Residues in contact with GLY 222 (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 VAL* 1.3 79.7 - - - +
223A ALA* 1.3 61.8 - - - -
224A GLY 3.3 2.5 - - - -
230A LEU 5.6 0.2 - - - +
231A LEU* 3.9 12.8 - - - +
232A THR* 5.1 1.4 + - - +
300A LYS 3.9 1.6 - - - -
302A GLY 3.3 16.4 - - - -
304A PRO* 3.6 15.1 - - - +
327A VAL* 2.9 17.0 + - - +
328A PRO 4.5 1.7 - - - +
329A GLY* 4.0 12.7 - - - -
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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