Contacts of the strand formed by residues 209 - 215 (chain B) in PDB entry 3L3T
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 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B SER* 3.8 23.1 - - - +
47B ILE* 4.3 15.5 - - + -
53B VAL* 4.5 12.6 - - + -
121B ILE* 3.9 13.1 - - + +
122B SER 3.0 18.4 + - - +
123B LEU* 5.1 1.3 - - + -
124B PRO* 3.0 28.3 - - + +
198B PRO* 3.5 32.1 - - + -
199B VAL 3.6 8.3 - - - +
200B VAL* 4.3 4.0 - - + -
204B GLN* 1.3 68.9 - - - +
210B GLN* 1.3 58.8 + - - +
211B GLY 3.5 20.0 - - - +
212B VAL* 5.3 0.9 - - + -
231B VAL* 3.5 23.9 - - + +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PRO* 3.7 16.0 - - + +
127B ALA* 2.8 26.3 + - - +
128B PRO* 3.9 6.6 + - - +
129B PRO* 3.5 37.5 - - + +
181B PHE* 3.5 14.0 - - + -
199B VAL* 2.9 10.7 + - + +
201B CYS* 3.9 36.4 + - + +
204B GLN* 3.4 14.8 + - - +
209B LEU* 1.3 75.4 - - - +
211B GLY* 1.3 58.6 + - - +
229B THR 3.5 1.2 - - - +
230B LYS* 3.8 0.5 - - - -
231B VAL* 3.0 25.2 + - - -
232B TYR* 4.4 3.6 - - - +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B PHE* 3.9 9.0 - - - -
198B PRO* 3.7 1.4 - - - +
199B VAL* 3.0 42.5 + - - +
209B LEU* 3.5 11.2 - - - +
210B GLN* 1.3 78.9 - - - +
212B VAL* 1.3 65.1 + - - +
228B TYR* 4.5 0.7 - - - -
229B THR 3.0 9.9 - - - -
231B VAL* 3.8 2.2 - - - +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 4.0 19.7 - - + +
54B SER 3.7 17.0 - - - +
55B ALA* 3.9 5.2 - - + +
102B ASP 4.7 1.6 - - - +
103B ILE* 4.4 5.4 - - + -
196B GLY* 3.4 37.2 - - - +
197B GLY 3.4 2.9 - - - -
209B LEU* 5.3 1.8 - - + -
211B GLY* 1.3 74.4 - - - +
213B VAL* 1.3 68.0 + - - +
214B SER* 3.1 2.3 + - - -
228B TYR* 3.3 5.1 - - - -
229B THR* 2.9 41.1 + - - +
231B VAL* 3.5 23.3 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 4.0 4.7 - - - +
138B ILE* 4.3 15.7 - - + -
139B SER 5.1 2.0 - - - +
190B SER* 3.5 27.6 - - - +
194B ASP* 3.5 30.3 - - + +
195B ALA* 3.6 10.5 - - - +
196B GLY 3.0 21.0 + - - -
197B GLY* 2.9 22.3 + - - +
198B PRO 4.6 1.1 - - - +
212B VAL* 1.3 74.3 - - - +
214B SER* 1.3 59.8 + - - +
228B TYR* 3.4 22.3 - - + -
15F LYS* 4.0 13.0 - - + +
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B HIS* 3.3 21.2 - - - -
99B LEU* 4.9 1.2 + - - +
102B ASP* 2.8 31.6 + - - +
180B MET* 6.0 1.4 - - - +
212B VAL* 3.1 8.2 + - - -
213B VAL* 1.3 75.3 - - - +
215B TRP* 1.3 79.5 + - - +
227B VAL* 3.2 18.0 + - - -
228B TYR* 4.2 2.0 - - - -
229B THR* 4.0 11.4 + - - -
14F CYS* 3.8 0.2 - - - -
15F LYS* 3.5 17.3 + - - +
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Residues in contact with TRP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B FMT 4.3 15.7 - - - -
99B LEU* 3.6 29.6 - - + +
172B TYR* 3.8 38.8 - + - -
175B LYS* 3.8 31.6 - - + -
176B ILE* 4.4 2.7 - - + -
180B MET* 3.5 37.3 - - + +
214B SER* 1.3 103.5 - - - +
216B GLY* 1.3 78.2 + - - +
217B HIS* 4.7 0.9 - - + -
227B VAL* 2.7 54.7 + - + +
13F PRO* 3.3 30.5 - - + +
14F CYS* 4.1 2.2 - - - -
15F LYS* 3.4 15.3 + - - +
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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