Contacts of the strand formed by residues 208 - 215 (chain I) in PDB entry 5DST
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 LEU 208 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178I LYS* 3.8 10.8 - - - -
179I VAL* 3.7 5.4 - - + +
180I ASP 3.6 27.1 - - - +
182I ILE* 4.0 17.4 - - + +
203I ALA 3.7 1.4 + - - -
204I ARG* 2.8 50.7 + - + +
205I ASP 4.9 1.4 - - - +
207I TRP* 1.3 72.0 - - - +
209I LYS* 1.3 73.5 + - - +
210I PRO 3.8 0.5 - - - -
212I GLY* 3.8 17.5 - - - +
213I LEU 3.9 10.1 - - - +
214I MET* 3.8 20.9 - - + -
281I TYR* 4.7 5.2 - - + -
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Residues in contact with LYS 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I LYS* 3.9 18.2 - - - +
178I LYS* 3.6 18.4 - - + -
179I VAL 2.9 18.4 + - - +
180I ASP* 2.8 36.7 + - - +
207I TRP 3.4 1.0 + - - -
208I LEU* 1.3 82.5 - - - +
210I PRO* 1.3 86.6 - - + +
211I GLY 3.2 3.9 + - - -
212I GLY* 2.9 30.2 + - - +
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Residues in contact with PRO 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B PRO* 5.1 17.5 - - + -
178I LYS* 4.8 10.5 - - + -
208I LEU 4.5 1.1 - - - +
209I LYS* 1.3 98.8 - - + +
211I GLY* 1.3 63.0 + - - +
212I GLY 3.2 0.3 + - - -
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Residues in contact with GLY 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I LYS* 3.2 7.0 + - - -
210I PRO* 1.3 71.6 - - - +
212I GLY* 1.3 66.9 + - - +
213I LEU* 4.1 10.7 - - - +
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Residues in contact with GLY 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180I ASP 3.3 15.3 - - - -
208I LEU* 3.8 10.7 - - - +
209I LYS* 2.9 27.3 + - - -
210I PRO 3.1 1.8 + - - -
211I GLY* 1.3 86.1 - - - +
213I LEU* 1.3 62.8 + - - +
281I TYR* 3.5 18.2 - - - -
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Residues in contact with LEU 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I VAL* 3.3 35.4 - - + -
113I LYS* 6.4 1.3 - - + -
180I ASP 3.3 4.8 + - - +
181I ILE* 3.4 14.3 - - + -
182I ILE 3.0 23.4 + - - -
208I LEU* 3.9 1.9 - - - +
211I GLY 4.1 8.7 - - - +
212I GLY* 1.3 79.2 - - - +
214I MET* 1.3 68.9 + - - +
215I PHE* 4.2 11.7 - - + -
281I TYR* 3.7 4.3 - - - +
317I LYS* 3.7 44.0 - - + -
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Residues in contact with MET 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182I ILE* 3.3 25.4 - - + +
200I VAL* 3.6 23.1 - - + -
204I ARG* 3.9 30.5 - - + -
208I LEU* 3.8 8.7 - - + -
213I LEU* 1.3 82.1 - - - +
215I PHE* 1.3 66.2 + - - +
216I PRO* 3.2 21.7 - - - +
217I ASP* 3.2 19.5 - - + +
280I ILE* 3.5 42.8 - - + +
281I TYR* 3.3 21.9 + - + -
315I PHE* 5.3 0.7 - - - -
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Residues in contact with PHE 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I TYR* 4.0 3.1 - - + -
102I SER* 3.4 45.1 - - - +
103I MET* 4.7 2.9 - - + -
106I ASN* 5.5 1.1 - - + -
109I VAL* 4.2 16.6 - - + -
110I PHE* 3.6 30.7 - + - -
181I ILE* 3.9 17.0 - - + -
182I ILE 2.9 7.5 + - - +
183I ILE* 3.4 17.2 - - + -
184I SER* 3.1 25.5 + - - +
213I LEU* 4.2 20.0 - - + -
214I MET* 1.3 80.5 - - - +
216I PRO* 1.3 62.0 - - - +
315I PHE* 3.7 16.4 - + + -
317I LYS* 4.9 11.9 - - + -
318I CYS* 4.2 12.3 - - - -
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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