Contacts of the strand formed by residues 195 - 201 (chain C) in PDB entry 3DLX
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 GLN 195 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C GOL 5.4 1.8 + - - -
158C PRO* 3.7 18.2 - - - +
191C GLU* 3.1 4.1 - - - +
192C PHE 2.8 32.0 + - - +
193C ASN 3.3 2.4 - - - +
194C GLY* 1.3 79.8 - - - +
196C HIS* 1.3 73.3 + - - +
197C PHE* 3.4 27.8 - - + -
431C SER 3.7 21.2 + - - -
432C SER* 5.5 0.2 - - - +
433C ALA* 5.4 9.1 - - - +
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Residues in contact with HIS 196 (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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161A TYR* 2.7 29.4 + + - -
196A HIS* 3.3 42.4 + + - -
158C PRO* 4.2 4.7 - - - +
161C TYR* 3.6 41.2 + + + +
189C VAL* 3.4 26.5 - - + -
190C ARG 3.8 2.2 - - - -
191C GLU* 3.9 21.5 - - + +
194C GLY 5.2 1.6 + - - -
195C GLN* 1.3 85.6 + - - +
197C PHE* 1.3 68.9 + - - +
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Residues in contact with PHE 197 (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 TYR* 3.9 17.0 - - + -
157C THR 3.3 9.4 - - - +
158C PRO* 3.2 41.7 - - + -
161C TYR* 5.0 1.6 - - - -
189C VAL* 3.3 6.8 - - - +
190C ARG 3.0 36.4 + - - +
192C PHE* 3.6 24.7 - + + -
195C GLN* 3.4 43.7 - - + -
196C HIS* 1.3 75.4 - - - +
198C ILE* 1.3 66.1 + - - +
151D GLY 4.4 2.5 - - - -
153D PRO* 3.5 36.8 - - + -
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Residues in contact with ILE 198 (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 TYR* 3.4 4.9 - - - -
157C THR* 2.9 41.5 + - + +
159C THR 3.3 22.7 - - - +
160C GLY 4.4 4.9 - - - -
161C TYR* 4.3 10.1 - - + -
165C VAL* 4.0 15.5 - - + -
166C GLN* 3.4 34.5 - - + -
187C ARG* 4.1 13.9 - - + -
188C GLU 3.2 7.0 - - - +
189C VAL* 3.8 7.9 - - + -
197C PHE* 1.3 80.1 - - - +
199C LEU* 1.3 61.0 + - - +
200C GLU* 3.5 24.9 + - + +
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Residues in contact with LEU 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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154C ALA* 3.8 26.2 - - + -
155C PHE* 3.5 14.4 - - - +
156C TYR* 3.5 38.9 - - + +
187C ARG* 3.5 25.1 - - - +
188C GLU* 2.9 52.0 + - + +
198C ILE* 1.3 72.9 - - - +
200C GLU* 1.3 61.0 + - - +
201C GLU* 5.5 4.5 - - + -
156D TYR* 4.2 8.3 - - + -
190D ARG* 3.5 17.5 - - - +
192D PHE* 4.9 1.8 - - + -
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Residues in contact with GLU 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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140C THR* 3.5 26.7 + - + +
144C ARG* 3.7 33.4 + - + -
154C ALA* 3.2 3.4 - - - -
155C PHE* 3.0 45.7 + - + +
157C THR* 3.7 20.2 - - + -
159C THR 4.9 0.3 - - - +
165C VAL* 3.9 8.1 - - - +
187C ARG* 3.2 32.7 + - - +
198C ILE* 3.5 17.4 - - + +
199C LEU* 1.3 75.4 - - - +
201C GLU* 1.3 64.9 + - - +
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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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144C ARG* 2.7 41.3 + - - +
153C PRO 3.4 10.9 - - - +
154C ALA* 4.3 8.7 - - + -
155C PHE* 5.1 0.7 - - - -
199C LEU* 5.5 5.2 - - + -
200C GLU* 1.3 78.6 + - - +
202C ALA* 1.3 67.9 + - - +
192D PHE* 3.7 25.1 - - + -
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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