Contacts of the strand formed by residues 311 - 318 (chain B) in PDB entry 1PZN
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 LEU 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.6 31.9 - - + +
128B ILE* 5.9 1.6 - - - -
129B GLU* 6.1 4.9 - - + -
133B ILE 3.2 3.1 + - - +
134B THR* 3.4 16.8 - - + +
135B GLU* 2.8 26.2 + - - +
309B ALA* 3.0 2.8 + - - +
310B THR* 1.3 83.8 - - + +
312B ARG* 1.3 71.2 + - - +
313B VAL* 4.0 10.1 - - + -
327B LEU* 4.0 27.1 - - + -
329B ASP* 4.6 13.0 - - + +
331B PRO 6.1 1.3 - - - +
333B LEU* 4.3 18.6 - - + -
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 2.7 45.9 + - - +
137B PHE* 3.1 38.3 - - + -
283B ASN* 4.9 0.2 + - - -
305B LEU* 3.4 37.5 - - - +
306B ALA 3.9 9.0 - - - -
307B HIS* 5.6 1.6 - - - +
309B ALA* 4.2 13.5 - - + +
311B LEU* 1.3 83.4 - - - +
313B VAL* 1.3 62.6 + - - +
327B LEU* 3.9 3.3 - - - -
328B ILE* 3.0 45.6 + - + +
329B ASP* 4.4 7.0 + - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 4.9 7.6 - - + -
124B LEU* 4.0 21.3 - - + -
134B THR* 4.2 10.5 - - + -
135B GLU 2.7 10.7 + - - +
136B VAL* 3.2 17.3 - - + +
137B PHE* 3.0 26.6 + - - -
147B LEU* 6.2 1.3 - - + -
311B LEU* 4.0 11.0 - - + -
312B ARG* 1.3 75.2 - - - +
314B TYR* 1.3 67.8 + - - +
315B LEU* 5.2 2.5 - - + -
325B ALA* 4.5 11.4 - - + -
326B ARG 3.4 16.4 - - - +
327B LEU* 3.9 20.4 - - + +
328B ILE* 3.5 1.8 - - - -
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Residues in contact with TYR 314 (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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137B PHE* 3.4 33.2 - + + -
138B GLY* 4.3 7.0 - - - -
139B GLU* 5.3 3.7 - - + +
285B VAL* 5.1 4.0 - - + -
313B VAL* 1.3 72.9 - - - +
315B LEU* 1.3 82.0 + - - +
316B ARG* 3.6 36.8 - - + +
324B ILE 3.9 0.6 - - - +
325B ALA* 3.6 0.5 - - - -
326B ARG* 2.8 66.2 + - + +
328B ILE* 2.9 25.1 - - + +
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Residues in contact with LEU 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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120B LEU* 5.8 0.2 - - + -
136B VAL* 3.2 31.0 - - + -
137B PHE 3.0 10.2 + - - +
138B GLY* 3.4 13.7 - - - -
139B GLU 4.3 0.3 + - - -
142B SER* 2.9 57.8 - - - +
143B GLY 5.2 0.7 - - - -
144B LYS* 4.2 14.4 - - + +
147B LEU* 4.0 17.0 - - + -
313B VAL* 5.2 2.7 - - + -
314B TYR* 1.3 80.5 - - - +
316B ARG* 1.3 63.2 + - - +
323B ARG* 5.5 0.2 - - + -
324B ILE 3.4 11.4 - - - +
325B ALA* 4.2 10.3 - - + -
340B PHE* 4.3 18.2 - - + -
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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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139B GLU* 5.7 5.2 - - + +
142B SER* 4.1 9.0 - - - -
314B TYR* 3.6 30.9 - - + +
315B LEU* 1.3 75.8 - - - +
317B LYS* 1.3 69.7 + - - +
323B ARG* 3.3 6.6 - - - +
324B ILE* 2.9 61.3 + - + +
326B ARG* 2.6 36.0 - - - +
337B GLU* 2.7 23.0 + - - -
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Residues in contact with LYS 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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140B PHE 4.9 6.5 + - - -
141B GLY* 3.8 24.7 + - - +
142B SER* 4.5 5.7 - - - +
316B ARG* 1.3 83.5 + - - +
318B GLY* 1.3 62.4 + - - +
319B LYS 5.9 0.9 - - - +
321B GLY* 5.9 0.7 - - - -
322B LYS 3.6 5.4 - - - +
323B ARG* 3.0 25.6 - - - +
365B IMD 4.2 23.8 + - + -
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Residues in contact with GLY 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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316B ARG 3.5 3.0 + - - -
317B LYS* 1.3 76.7 - - - +
319B LYS* 1.3 75.7 + - - +
320B GLY 3.4 0.2 + - - -
321B GLY 3.9 0.2 + - - -
322B LYS* 2.7 38.5 + - - +
323B ARG* 3.9 0.6 - - - +
324B ILE* 4.4 15.5 - - - -
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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