Contacts of the strand formed by residues 197 - 204 (chain C) in PDB entry 3Q3G
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 SER 197 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LYS 3.8 1.1 - - - +
156C ILE* 3.5 4.5 - - - +
157C ASP* 2.8 48.7 + - - +
158C GLY 5.4 1.6 - - - -
196C ASN* 1.4 73.4 - - - +
198C TYR* 1.4 62.6 + - - +
199C THR* 4.6 4.8 - - - +
214C SER* 3.1 22.3 + - - -
215C PHE 3.4 6.0 + - - -
216C ASN* 3.5 20.2 + - - +
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Residues in contact with TYR 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE* 3.5 7.3 - - + +
138C VAL* 4.0 14.6 - - + -
154C TRP* 5.2 1.1 - + + -
155C LYS 3.5 1.8 - - - -
156C ILE* 3.6 37.5 - - + -
185C LEU* 4.3 5.6 - - + -
187C LEU* 4.1 17.5 - - + +
192C TYR* 3.0 50.2 + + - -
195C HIS* 3.5 33.7 + - + -
196C ASN 3.9 7.4 - - - -
197C SER* 1.4 76.6 - - - +
199C THR* 1.3 62.0 + - - +
214C SER* 2.9 2.9 + - - -
215C PHE* 2.8 65.4 + + + -
217C ARG* 4.8 0.9 - - + -
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Residues in contact with THR 199 (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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123C ILE* 3.8 1.7 - - - +
153C LYS 3.8 0.2 - - - +
154C TRP* 3.2 13.0 - - - -
155C LYS* 2.7 68.8 + - + +
158C GLY* 5.5 4.5 - - - +
197C SER* 4.6 6.1 - - - +
198C TYR* 1.3 76.5 - - - +
200C CYS* 1.3 65.3 + - - +
201C GLU* 4.2 2.1 + - - +
212C VAL* 3.3 22.0 - - + +
213C LYS 3.3 14.2 + - - -
214C SER* 3.4 17.7 - - - +
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Residues in contact with CYS 200 (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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121C VAL* 4.0 10.3 - - - +
123C ILE* 4.0 14.1 - - - +
140C CYS* 2.0 53.8 - - + -
152C VAL* 5.0 4.9 - - + -
153C LYS 3.3 6.3 - - - +
154C TRP* 3.9 15.5 - - + +
199C THR* 1.3 76.4 + - - +
201C GLU* 1.3 60.9 + - - +
202C ALA 4.0 0.6 + - - -
211C ILE 3.7 2.8 - - - +
212C VAL* 3.8 0.3 - - - -
213C LYS* 3.0 36.1 + - - +
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Residues in contact with GLU 201 (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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151C ASN 3.6 0.7 - - - +
152C VAL* 3.3 6.7 - - - +
153C LYS* 2.7 73.0 + - + +
155C LYS* 3.3 38.1 + - + +
199C THR* 4.2 2.8 + - - +
200C CYS* 1.3 71.8 - - - +
202C ALA* 1.3 60.2 + - - +
203C THR* 4.0 3.7 + - - +
210C PRO* 3.3 29.8 - - + +
211C ILE 3.5 2.7 - - - -
212C VAL* 3.6 26.7 - - + +
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Residues in contact with ALA 202 (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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119C PRO* 4.6 9.0 - - + -
121C VAL* 3.8 26.5 - - + -
142C LEU* 3.8 22.7 - - + -
150C ILE* 5.0 0.9 - - + -
151C ASN 3.4 4.3 - - - -
200C CYS 4.0 0.6 + - - -
201C GLU* 1.3 71.2 - - - +
203C THR* 1.3 63.1 + - - +
204C HIS* 4.1 1.8 + - - -
210C PRO* 3.3 5.1 - - - +
211C ILE* 2.7 48.3 + - + +
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Residues in contact with THR 203 (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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150C ILE* 3.6 4.3 - - - +
151C ASN* 2.7 54.7 + - - +
153C LYS* 5.5 7.6 - - - +
201C GLU* 4.4 6.8 + - - +
202C ALA* 1.3 72.6 - - - +
204C HIS* 1.3 65.2 + - - +
207C SER 5.5 2.9 - - - +
208C THR 5.5 6.1 - - - +
210C PRO* 4.1 20.4 - - + +
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Residues in contact with HIS 204 (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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117C ALA 3.3 13.8 + - - -
119C PRO* 4.0 14.0 - - + +
145C PHE* 3.8 5.2 - + + -
146C TYR 3.2 24.4 - - - -
147C PRO* 2.9 30.4 + - + +
149C ASP 3.2 24.9 + - - -
150C ILE* 3.7 23.8 - - + -
202C ALA 4.1 2.5 + - - +
203C THR* 1.3 76.6 - - - +
205C LYS* 1.4 61.2 + - - +
206C THR* 2.8 35.8 + - + +
207C SER* 2.8 31.9 + - - +
210C PRO* 5.8 0.4 - - - +
211C ILE* 6.0 1.6 - - + -
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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