Contacts of the strand formed by residues 212 - 217 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C SER* 3.8 2.3 + - - -
54C LEU* 2.8 36.3 + - + -
55C ASN* 3.0 11.8 + - - +
58C TRP* 4.0 23.3 - - + -
86C VAL* 4.3 6.7 - - + -
141C ILE* 4.0 18.6 - - + -
142C ILE 3.4 9.6 - - - +
143C PHE* 3.8 25.1 - - + -
208C ILE* 3.6 32.3 - - + -
210C ARG 4.1 1.1 - - - +
211C ASP* 1.3 73.9 - - - +
213C SER* 1.3 69.7 + - - +
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Residues in contact with SER 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 3.9 20.8 - - - +
52C ARG 3.0 19.7 - - - -
53C SER* 4.3 2.7 - - - -
54C LEU* 4.1 6.5 - - - +
141C ILE* 3.4 8.0 - - - +
142C ILE* 2.8 49.7 + - - +
144C ASP* 5.1 4.9 + - - -
211C ASP* 5.5 3.9 - - - +
212C VAL* 1.3 78.1 - - - +
214C LEU* 1.3 59.4 - - - +
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLN 3.6 1.4 - - - +
51C LEU* 3.6 3.9 - - - +
52C ARG* 2.8 69.2 + - + +
54C LEU* 4.1 19.5 - - + -
127C PHE* 3.9 23.3 - - + -
129C VAL* 4.3 6.3 - - + -
133C TRP* 3.8 13.8 - - + -
139C THR* 3.9 21.1 - - + -
140C ARG 3.4 11.2 - - - +
141C ILE* 4.0 18.2 - - + -
173C LEU* 4.3 11.9 - - + -
177C LEU* 5.4 0.4 - - + -
213C SER* 1.3 74.1 - - - +
215C LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C HIS* 5.3 1.1 - - + -
33C PHE* 3.8 26.9 - - + +
34C ALA* 3.6 37.2 - - - +
35C SER* 4.0 2.2 - - - +
50C GLN 3.3 11.7 - - - +
51C LEU* 4.2 8.7 - - + -
133C TRP* 4.0 3.4 - - - -
138C GLN 3.5 2.4 - - - +
139C THR* 3.6 0.2 - - - -
140C ARG* 3.0 59.9 + - + +
142C ILE* 4.0 17.4 - - + +
213C SER 4.3 0.2 - - - -
214C LEU* 1.3 74.5 - - - +
216C HIS* 1.3 64.3 + - - +
217C LYS* 3.8 23.9 - - + +
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Residues in contact with HIS 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C SER* 3.1 17.0 - - - -
37C ARG* 2.8 36.5 + - - +
50C GLN* 3.0 12.1 + - + +
133C TRP* 3.0 49.4 + - + -
136C GLU* 2.8 31.2 + - + -
137C GLY* 3.8 5.3 - - - -
138C GLN 3.2 12.8 - - - -
139C THR* 3.7 7.6 - - - -
215C LEU* 1.3 74.0 - - - +
217C LYS* 1.3 72.4 + - - +
218C PRO* 4.7 1.8 - - + -
8504C DMS 3.5 32.9 - - + +
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Residues in contact with LYS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C PHE* 3.7 18.2 - - - -
35C SER* 3.7 10.8 - - - -
37C ARG* 3.8 2.9 - - - -
137C GLY* 3.4 2.1 - - - -
138C GLN* 2.7 44.9 + - - +
140C ARG* 4.4 5.8 - - - +
215C LEU* 3.8 21.7 + - + +
216C HIS* 1.3 77.0 - - - +
218C PRO* 1.3 67.8 - - + +
221C GLN* 3.6 25.1 - - - +
222C ILE 2.9 23.2 + - - -
324C GLU* 2.7 36.8 + - - +
326C GLU* 2.9 24.4 + - - +
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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