Contacts of the strand formed by residues 544 - 549 (chain 0) in PDB entry 5OA3
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 544 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5070 VAL 4.5 2.3 - - - +
5080 ARG* 4.7 0.5 - - - +
5090 ASN 4.6 10.9 + - - -
5100 LEU* 5.2 4.5 + - - +
5110 GLU* 3.0 26.8 + - - +
5170 PRO* 3.8 26.4 - - + +
5180 TYR* 3.7 35.7 - - + +
5340 VAL* 4.0 15.0 - - + +
5350 ASN 3.6 13.0 - - - +
5360 PRO* 4.6 4.7 - - + -
5370 ALA* 4.0 4.5 - - - +
5420 ASP 3.5 17.9 - - - +
5430 SER* 1.3 77.2 - - - +
5450 GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 545 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4980 ARG* 4.7 4.6 - - - +
5060 VAL* 3.7 14.9 - - + +
5070 VAL 3.3 12.8 - - - +
5080 ARG* 2.9 43.9 + - + +
5340 VAL* 3.5 4.6 - - - +
5350 ASN* 2.9 44.9 + - + +
5360 PRO 3.7 16.0 + - - +
5370 ALA* 3.7 3.5 - - + +
5380 PRO* 3.4 9.4 - - - +
5440 LEU* 1.3 75.0 - - - +
5460 VAL* 1.3 64.8 + - - +
5470 GLN* 2.9 29.2 + - + +
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Residues in contact with VAL 546 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5050 THR 3.4 2.3 - - - +
5060 VAL* 3.4 2.4 - - - -
5070 VAL* 2.9 41.4 + - + +
5100 LEU* 3.9 23.1 - - + -
5170 PRO* 3.3 33.0 - - + +
5200 VAL* 4.9 1.1 - - + -
5210 ALA* 4.0 22.9 - - + +
5240 LEU* 4.4 7.0 - - + -
5320 THR* 5.0 0.9 - - - -
5330 THR 3.5 8.1 - - - +
5340 VAL* 4.1 5.6 - - + -
5450 GLN* 1.3 76.5 - - - +
5470 GLN* 1.3 65.2 + - - +
5480 ILE* 3.8 20.8 - - + +
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Residues in contact with GLN 547 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4980 ARG* 3.2 32.0 + - - +
5040 VAL* 4.0 11.0 - - + +
5050 THR 3.4 3.1 - - - -
5060 VAL* 3.7 18.2 - - + -
5310 SER 3.9 0.7 - - - +
5320 THR* 3.2 5.5 - - - -
5330 THR* 2.9 47.2 + - - +
5350 ASN* 3.2 26.3 + - - +
5450 GLN* 2.9 28.3 + - + +
5460 VAL* 1.3 73.7 - - - +
5480 ILE* 1.3 62.8 + - - +
10582 A 5.9 0.4 + - - -
10592 G 5.1 11.5 + - - -
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Residues in contact with ILE 548 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5040 VAL* 3.3 6.5 - - - +
5050 THR* 2.9 46.1 + - - +
5070 VAL* 4.1 10.8 - - + -
5240 LEU* 3.6 30.3 - - + -
5280 CYS* 4.2 11.7 - - + -
5300 ALA* 5.0 3.8 - - + -
5310 SER 3.9 2.5 - - - +
5320 THR* 3.8 24.0 - - + -
5460 VAL* 3.8 15.0 - - + +
5470 GLN* 1.3 79.0 - - - +
5490 GLN* 1.3 66.2 + - - +
5500 GLY 3.3 2.6 + - - +
5520 GLN* 3.4 31.2 - - + -
5560 LEU* 4.5 9.0 - - + -
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Residues in contact with GLN 549 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5020 LYS* 6.4 1.1 - - + -
5030 LYS 4.3 4.7 - - - +
5040 VAL* 4.9 6.7 - - + +
5300 ALA* 3.7 17.0 - - + +
5310 SER* 3.1 45.3 + - - +
5480 ILE* 1.3 77.4 - - - +
5500 GLY* 1.3 57.4 + - - +
5520 GLN* 3.8 6.2 + - - -
10582 A 3.3 21.3 + - + +
10592 G 3.9 20.2 + - - +
18282 C 3.4 19.3 + - - +
18292 G 2.3 35.6 + - - +
18492 G 4.5 3.1 - - - +
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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