Contacts of the strand formed by residues 244 - 248 (chain 9) in PDB entry 2J28
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 GLY 244 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2179 THR 3.4 4.4 + - - -
2189 LEU* 3.1 23.0 - - - +
2429 LEU 2.8 9.6 + - - -
2439 THR* 1.3 72.9 - - - +
2459 VAL* 1.3 73.2 + - - +
2699 PRO* 2.9 18.8 - - - -
2719 LYS* 4.8 18.2 - - - -
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Residues in contact with VAL 245 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2189 LEU* 4.5 3.6 - - - -
2199 PHE* 2.8 41.7 - - + +
2369 PHE* 4.2 3.6 - - + -
2449 GLY* 1.3 79.7 - - - +
2469 VAL* 1.3 64.5 + - - +
2639 ARG* 3.2 18.4 - - - +
2689 LYS* 2.6 49.8 - - + +
2699 PRO 2.3 25.2 + - - +
2709 ILE* 2.7 32.9 - - + +
2719 LYS* 3.0 9.1 + - - +
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Residues in contact with VAL 246 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169 SER* 4.8 8.3 - - - +
2189 LEU* 4.8 8.3 - - + -
2199 PHE 3.7 0.2 + - - -
2209 VAL* 3.0 45.7 - - + -
2459 VAL* 1.3 83.1 - - - +
2479 LEU* 1.3 64.0 + - - +
2489 THR* 5.1 1.8 - - + +
2639 ARG* 3.2 15.5 + - - +
2709 ILE* 3.9 7.6 - - - -
2719 LYS* 4.1 2.2 - - + +
2729 PHE* 3.2 56.3 - - + +
2739 LEU* 4.4 2.5 - - - +
2829 LEU* 5.8 1.1 - - + -
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Residues in contact with LEU 247 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2219 VAL* 3.0 9.4 - - + +
2239 ALA* 4.9 6.3 - - + +
2469 VAL* 1.3 74.7 - - - +
2489 THR* 1.3 70.3 + - - +
2499 LYS 4.3 0.2 - - - +
2569 GLY* 6.2 0.2 - - - -
2599 ALA* 3.8 12.8 - - + -
2609 LEU* 3.1 37.9 - - + +
2639 ARG* 1.0 121.1 - - + +
2709 ILE* 5.5 2.9 - - + -
2729 PHE 4.3 1.0 + - - -
2739 LEU* 3.0 48.0 - - + +
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Residues in contact with THR 248 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119 ALA 3.3 26.7 + - - +
1129 GLY* 3.9 15.0 - - - -
1169 SER* 5.4 4.0 - - - -
2209 VAL* 3.7 15.7 - - + -
2219 VAL 2.3 36.8 + - - +
2229 ASP* 2.6 47.0 + - - +
2239 ALA 3.3 1.9 + - - -
2469 VAL* 4.0 2.2 + - + -
2479 LEU* 1.3 72.2 - - - +
2499 LYS* 1.3 75.1 + - - +
2739 LEU 4.8 1.3 - - - -
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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