Contacts of the strand formed by residues 212 - 217 (chain B) in PDB entry 1JZ3
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 VAL 212 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B SER* 3.6 2.6 + - - -
54B LEU* 2.7 39.0 + - + -
55B ASN* 3.2 11.8 + - - +
58B TRP* 4.0 25.6 - - + -
86B VAL* 4.3 6.3 - - + -
141B ILE* 4.0 15.7 - - + -
142B ILE 3.2 7.2 - - - +
143B PHE* 3.8 28.9 - - + -
208B ILE* 3.5 31.6 - - + -
210B ARG 4.2 0.7 - - - +
211B ASP* 1.4 76.3 - - - +
213B SER* 1.3 60.4 + - - +
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Residues in contact with SER 213 (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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51B LEU* 4.0 15.3 - - - +
52B ARG 3.1 19.1 - - - -
53B SER* 4.4 2.0 - - - -
54B LEU* 4.1 4.0 - - - +
141B ILE* 3.3 7.3 - - - +
142B ILE* 2.7 57.8 + - - +
144B ASP* 5.2 3.5 + - - -
211B ASP* 5.5 4.7 - - - -
212B VAL* 1.3 78.0 - - - +
214B LEU* 1.4 60.8 + - - +
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Residues in contact with LEU 214 (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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50B GLN 3.5 1.7 - - - +
51B LEU* 3.4 6.1 - - - +
52B ARG* 2.8 66.4 + - + +
54B LEU* 3.8 25.8 - - + -
127B PHE* 4.0 22.7 - - + -
129B VAL* 4.7 5.8 - - + -
133B TRP* 3.6 18.7 - - + -
139B THR* 4.3 12.8 - - + -
140B ARG 3.2 13.9 - - - +
141B ILE* 4.0 18.8 - - + -
173B LEU* 4.4 10.1 - - + -
177B LEU* 5.4 0.9 - - + -
213B SER* 1.4 73.2 - - - +
215B LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 215 (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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30B HIS* 5.3 1.6 - - + -
33B PHE* 4.0 21.3 - - + +
34B ALA* 3.8 29.6 - - - +
35B SER 4.2 1.8 - - - +
50B GLN 3.4 13.9 - - - +
51B LEU* 3.9 15.0 - - + -
133B TRP* 3.9 3.6 - - - -
138B GLN 3.5 2.3 - - - +
139B THR* 3.6 0.2 - - - -
140B ARG* 2.8 57.0 + - + +
142B ILE* 4.0 22.2 - - + -
213B SER 4.2 0.4 + - - -
214B LEU* 1.3 75.5 - - - +
216B HIS* 1.3 64.1 + - - +
217B LYS* 3.8 28.6 + - + -
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Residues in contact with HIS 216 (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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35B SER* 3.1 17.0 - - - -
37B ARG* 2.9 38.2 + - - +
50B GLN* 3.0 14.5 + - + +
133B TRP* 3.0 55.8 + - + -
136B GLU* 2.9 32.6 + - + -
137B GLY* 3.8 5.5 - - - -
138B GLN 3.3 7.0 - - - -
139B THR* 3.5 11.7 - - - -
215B LEU* 1.3 73.1 - - - +
217B LYS* 1.3 74.1 + - - +
218B PRO* 4.6 1.3 - - + -
8504B DMS 3.7 25.5 - - + +
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Residues in contact with LYS 217 (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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33B PHE* 3.7 17.6 - - - -
35B SER* 3.7 11.9 - - - -
37B ARG* 3.8 3.1 - - - -
137B GLY* 3.3 1.9 - - - -
138B GLN* 2.6 52.2 + - - +
140B ARG* 4.2 7.6 - - - +
215B LEU* 3.8 23.5 + - + +
216B HIS* 1.3 78.0 - - - +
218B PRO* 1.3 65.4 - - + +
221B GLN* 3.5 25.1 - - - +
222B ILE 2.8 23.0 + - - -
324B GLU* 2.7 32.2 + - - +
326B GLU* 2.9 23.1 + - - +
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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