Contacts of the strand formed by residues 27 - 36 (chain 7) in PDB entry 4UOW
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 ALA 27 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197 PHE 3.3 11.9 - - - +
207 VAL* 4.2 14.8 - - + -
217 VAL 5.5 0.2 - - - +
267 ASP* 1.3 73.6 - - - +
287 THR* 1.3 62.7 + - - +
297 LEU* 5.7 0.7 - - + -
687 THR* 3.4 3.6 - - - -
697 ILE* 2.7 48.1 + - + +
727 LEU* 3.8 32.1 - - + -
977 LEU* 5.3 2.0 - - + -
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Residues in contact with THR 28 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 LYS 3.3 3.1 - - - +
187 ALA* 3.3 2.1 - - - -
197 PHE* 2.7 53.1 + - - +
267 ASP* 5.6 1.1 - - + -
277 ALA* 1.3 80.6 - - - +
297 LEU* 1.3 64.7 + - - +
307 SER* 3.9 6.9 + - - -
667 ARG* 3.8 26.0 - - + +
677 LEU 3.4 3.1 - - - -
687 THR* 3.5 28.3 - - + +
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Residues in contact with LEU 29 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 LYS 3.5 4.3 - - - -
187 ALA* 3.8 19.3 - - + -
277 ALA 5.4 0.2 - - - -
287 THR* 1.3 77.0 - - - +
307 SER* 1.3 56.8 + - - +
437 TRP* 3.8 28.8 - - + -
667 ARG* 3.4 1.4 - - - -
677 LEU* 2.8 48.2 + - + +
697 ILE* 3.8 21.1 - - + -
807 TYR* 3.4 46.2 - - + -
957 VAL* 3.8 18.2 - - + -
977 LEU* 4.2 11.4 - - + -
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Residues in contact with SER 30 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 THR* 4.9 1.6 - - - +
157 ARG 3.8 1.4 - - - +
167 PRO* 4.2 0.7 - - - -
177 LYS* 2.9 40.7 + - - +
197 PHE* 5.6 1.0 - - - +
287 THR* 3.9 15.1 + - - -
297 LEU* 1.3 75.9 - - - +
317 CYS* 1.3 64.0 + - - +
647 LEU* 5.2 11.4 - - - -
657 TYR 3.4 11.0 - - - -
667 ARG* 4.2 12.9 - - - +
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Residues in contact with CYS 31 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127 PHE* 3.9 6.1 - - + -
147 THR* 3.3 24.7 - - - +
157 ARG 3.9 0.2 - - - -
167 PRO* 3.7 18.2 - - + -
307 SER* 1.3 77.3 - - - +
327 GLN* 1.4 60.2 + - - +
337 ILE* 3.7 25.1 + - - -
437 TRP* 4.1 7.4 - - - -
637 ASP 3.8 0.2 - - - +
647 LEU* 3.6 8.3 - - - +
657 TYR* 2.9 37.1 + - - +
827 CYS* 3.9 17.7 - - - -
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Residues in contact with GLN 32 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127 PHE* 3.5 3.6 - - - -
137 LEU* 2.7 59.9 + - + +
147 THR* 3.4 32.0 + - - +
317 CYS* 1.4 71.3 - - - +
337 ILE* 1.3 58.0 + - - +
637 ASP* 3.2 38.6 + - - +
647 LEU* 4.6 14.4 - - + +
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Residues in contact with ILE 33 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117 ARG 3.6 13.9 - - - +
127 PHE* 3.6 36.3 - - + -
317 CYS* 3.7 17.0 + - - -
327 GLN* 1.3 78.4 - - - +
347 VAL* 1.3 73.1 + - - +
397 PRO* 3.8 12.5 - - + +
417 VAL* 3.6 25.8 - - + -
637 ASP* 2.8 22.6 + - - +
657 TYR* 3.3 32.0 + - + -
827 CYS* 3.9 2.9 - - - -
847 ALA* 3.6 22.4 - - + -
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Residues in contact with VAL 34 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97 ALA 4.0 1.0 - - - +
107 PRO* 3.3 4.3 - - - +
117 ARG* 3.0 52.1 + - + +
137 LEU* 3.5 45.3 - - + -
337 ILE* 1.3 77.8 - - - +
357 GLY* 1.3 60.0 + - - +
397 PRO* 3.6 6.3 - - - +
637 ASP* 3.8 18.2 - - + +
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Residues in contact with GLY 35 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87 SER* 4.0 13.5 - - - -
97 ALA 4.1 6.5 - - - -
107 PRO* 4.4 0.2 - - - -
347 VAL* 1.3 76.8 - - - +
367 ASN* 1.3 62.5 + - - +
377 PRO 3.2 12.5 - - - +
387 THR* 3.3 18.9 + - - +
397 PRO* 3.8 11.0 - - - +
867 ASN* 4.3 1.6 - - - -
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Residues in contact with ASN 36 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77 SER* 3.3 26.6 + - - +
87 SER* 2.7 46.7 + - - +
357 GLY* 1.3 75.8 + - - -
377 PRO* 1.4 65.5 + - - +
387 THR* 5.2 7.3 - - - +
867 ASN* 3.5 1.6 - - - -
887 ILE* 3.3 3.8 - - - +
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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