Contacts of the strand formed by residues 240 - 244 (chain H) in PDB entry 3SZ9
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 LYS 240 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H VAL* 3.9 20.6 - - + -
161H VAL 3.4 1.6 + - - -
162H CYS* 3.3 8.6 - - + -
163H GLY 2.6 33.1 + - - -
238H VAL* 3.5 5.6 - - - +
239H ASP* 1.3 82.6 - - - +
241H VAL* 1.3 66.9 + - - +
242H ALA* 4.1 4.3 - - - +
263H LYS* 4.3 1.8 - - - -
264H ARG* 3.1 20.3 - - + +
265H VAL 4.2 1.2 - - - -
266H THR* 2.6 41.8 + - - +
484H ALA* 3.9 19.8 + - - +
485H TYR* 3.5 43.3 - - + +
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Residues in contact with VAL 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163H GLY* 3.1 13.2 - - - +
165H ILE* 4.3 21.5 - - + -
232H ILE* 4.6 7.6 - - + -
233H ALA* 4.7 6.7 - - - -
238H VAL* 5.1 0.7 - - + -
240H LYS* 1.3 80.3 + - - +
242H ALA* 1.3 65.3 + - - +
243H PHE 4.7 0.2 - - - +
253H ILE* 3.7 27.4 - - + +
257H ALA* 5.0 0.7 - - + -
263H LYS* 3.9 19.2 - - + +
264H ARG 2.9 7.6 + - - +
265H VAL* 3.5 28.8 - - + -
266H THR 3.1 21.1 + - - +
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Residues in contact with ALA 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H GLY 2.8 11.3 + - - +
164H GLN* 3.6 2.3 - - + -
165H ILE* 3.0 25.5 + - - +
178H LYS* 3.6 21.9 - - + +
240H LYS* 4.1 3.5 - - + +
241H VAL* 1.3 75.5 - - - +
243H PHE* 1.3 59.7 + - - +
266H THR* 3.4 20.4 - - - +
476H GLU* 5.5 0.7 - - - +
485H TYR* 3.5 25.1 - - + +
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Residues in contact with PHE 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ILE* 3.6 35.0 - - + -
178H LYS* 4.9 0.6 + - - -
241H VAL* 4.1 1.0 - - + +
242H ALA* 1.3 74.4 - - - +
244H THR* 1.3 70.3 + - - +
245H GLY* 3.6 25.4 - - - -
246H SER 3.6 22.4 - - - -
249H ILE* 3.6 29.6 - - + -
250H GLY* 3.7 15.5 - - - -
253H ILE* 3.7 22.4 - - + -
266H THR 3.1 7.3 + - - -
267H LEU* 3.3 17.0 - - + -
268H GLU* 2.9 24.3 + - - +
269H LEU* 3.8 12.8 - - + -
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Residues in contact with THR 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ILE* 3.1 10.9 + - - +
166H ILE* 4.4 1.5 - - - -
167H PRO* 3.7 42.2 - - + +
174H MET* 4.4 15.7 - - - -
178H LYS* 2.8 30.5 + - - -
243H PHE* 1.3 88.6 + - - +
245H GLY* 1.3 61.8 + - - +
268H GLU* 3.2 25.7 - - + +
302H CYS* 6.3 0.2 - - + -
476H GLU* 4.3 1.1 + - - +
8001H I3E 4.8 12.1 - - + -
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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