Contacts of the strand formed by residues 214 - 219 (chain C) in PDB entry 1GZH
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 HIS 214 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C MET* 3.4 23.9 - - - +
161C ALA 4.7 1.7 + - - +
172C VAL* 4.8 3.7 - - + +
173C VAL 4.0 15.7 + - - +
174C ARG* 3.6 36.7 + - + -
192C GLN* 3.2 41.6 + - + +
193C HIS* 3.5 21.3 - + + -
194C LEU 4.7 2.4 + - - +
206C LEU 3.5 4.0 - - - -
207C ASP* 3.3 26.2 + - - -
212C PHE 3.6 15.2 + - - -
213C ARG* 1.3 73.0 - - - +
215C SER* 1.3 64.3 + - - +
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Residues in contact with SER 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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158C ARG* 2.7 54.8 + - - +
159C ALA 3.3 8.4 + - - -
160C MET* 3.9 14.3 - - - +
193C HIS* 4.0 5.0 - - - -
195C ILE 5.7 0.2 - - - -
205C TYR* 3.7 2.1 - - - -
206C LEU* 2.9 39.5 + - - +
213C ARG 4.8 1.1 - - - -
214C HIS* 1.3 77.8 - - - +
216C VAL* 1.3 59.8 + - - +
217C VAL 4.3 0.2 - - - -
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Residues in contact with VAL 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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157C VAL 3.7 1.0 - - - +
158C ARG* 3.5 1.7 - - - -
159C ALA* 2.8 49.1 + - + +
195C ILE* 3.7 33.4 - - + +
197C VAL* 3.6 15.9 - - + -
203C VAL* 3.4 29.8 - - + -
204C GLU 3.6 4.0 - - - +
205C TYR* 3.7 15.7 - - + -
215C SER* 1.3 75.4 - - - +
217C VAL* 1.3 63.8 + - - +
234C TYR* 4.2 7.4 + - + -
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Residues in contact with VAL 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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156C ARG* 3.4 58.6 - - + +
157C VAL 3.2 16.6 - - - +
158C ARG* 4.1 20.9 - - - +
202C ARG 4.2 0.3 - - - +
203C VAL* 3.7 0.3 - - - +
204C GLU* 2.9 53.2 + - + +
206C LEU* 6.1 2.2 - - + -
215C SER 4.3 0.4 - - - +
216C VAL* 1.3 73.6 - - - +
218C VAL* 1.3 70.8 + - - +
258C GLU* 4.3 8.1 - - - +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ARG* 3.5 5.2 - - - +
157C VAL* 2.9 34.9 + - + +
197C VAL* 4.2 16.8 - - + -
200C ASN* 2.9 31.9 - - + +
203C VAL* 3.9 19.1 - - + -
217C VAL* 1.3 86.1 - - - +
219C PRO* 1.3 74.1 - - - +
221C GLU* 5.3 0.7 - - - +
232C ILE* 4.2 29.6 - - + -
234C TYR* 5.7 0.7 - - - +
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Residues in contact with PRO 219 (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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155C THR 3.9 5.2 - - - +
156C ARG* 4.4 15.3 - - + +
200C ASN* 3.8 3.1 - - - +
202C ARG* 3.5 58.1 - - + +
218C VAL* 1.3 95.7 - - + +
220C TYR* 1.3 62.6 + - - +
221C GLU* 2.4 33.2 + - + +
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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