Contacts of the strand formed by residues 425 - 432 (chain D) in PDB entry 5UHF
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 SER 425 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1043C ALA* 3.3 1.4 - - - +
1044C ARG* 2.8 30.3 + - - +
1065C GLY* 3.6 2.9 - - - -
1066C GLN* 3.0 19.5 + - - -
422D VAL* 3.0 24.7 + - - -
423D ASP 4.0 0.2 - - - -
424D TYR* 1.3 77.3 - - - +
426D GLY* 1.3 57.8 + - - +
451D LEU* 3.4 7.6 - - - +
543D VAL 3.1 13.9 - - - -
544D HIS* 3.4 25.4 - - - -
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Residues in contact with GLY 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042C HIS 3.2 12.8 - - - -
1043C ALA* 3.6 4.5 - - - -
1066C GLN* 3.2 17.9 - - - +
425D SER* 1.3 76.1 - - - +
427D ARG* 1.3 58.7 + - - +
447D MET* 3.7 12.6 - - - -
542D ALA* 3.4 0.3 - - - -
543D VAL* 2.6 41.1 + - - +
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Residues in contact with ARG 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040C LYS 3.2 8.0 - - - +
1042C HIS* 2.7 35.8 + - + +
1066C GLN* 3.2 26.8 + - + +
426D GLY* 1.3 75.5 - - - +
428D SER* 1.3 62.9 + - - +
447D MET* 3.9 4.2 - - - +
499D ASN* 5.8 0.6 + - - -
501D ALA* 4.7 13.1 - - - +
540D GLN* 3.3 55.4 + - + +
541D MET 3.2 15.5 - - - +
542D ALA* 4.4 15.5 - - - +
543D VAL* 5.0 0.7 - - - -
16G C 3.9 48.1 + - - +
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Residues in contact with SER 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037C VAL* 4.7 0.7 - - - +
1040C LYS 4.3 3.4 - - - -
1041C ILE* 3.4 30.1 + - - +
427D ARG* 1.3 80.6 - - - +
429D VAL* 1.3 75.8 + - - +
430D ILE* 3.7 0.5 + - - +
447D MET* 4.0 2.7 - - - -
520D LYS 3.0 23.0 + - - -
522D ILE* 3.4 28.9 - - - +
540D GLN* 4.3 6.5 - - - -
541D MET 3.3 20.8 + - - -
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Residues in contact with VAL 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882C GLY* 4.1 15.9 - - - +
894C VAL* 4.1 10.3 - - + -
1035C HIS 5.8 0.7 - - - +
1037C VAL* 3.9 27.4 - - + +
1040C LYS* 3.7 35.9 - - + -
428D SER* 1.3 78.5 + - - +
430D ILE* 1.3 71.3 + - - +
521D ALA* 3.8 3.2 - - - -
522D ILE* 2.9 25.5 + - - +
538D GLY* 4.0 17.0 - - - +
539D ASP 3.3 15.7 - - - +
540D GLN* 4.3 3.7 - - + +
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Residues in contact with ILE 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C VAL* 3.8 10.0 - - - +
428D SER 4.1 1.3 - - - +
429D VAL* 1.3 79.9 - - - +
431D VAL* 1.3 68.5 + - - +
522D ILE* 3.2 14.8 - - + +
524D LEU* 4.3 12.3 - - + -
534D ALA* 4.0 19.3 - - + -
535D ASP 3.8 7.2 - - - +
536D PHE* 3.4 28.7 - - + -
539D ASP* 3.1 39.2 + - + +
541D MET* 3.6 43.5 - - + +
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Residues in contact with VAL 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881C ASP* 4.5 2.9 - - + -
882C GLY* 3.7 22.7 - - - +
894C VAL* 4.6 5.8 - - + -
895C ILE 3.8 4.7 - - - +
896C GLY* 3.3 31.6 - - - +
430D ILE* 1.3 82.4 - - - +
432D VAL* 1.3 75.9 + - - +
521D ALA* 3.6 25.6 - - + -
522D ILE 2.7 12.0 + - - +
523D GLN* 3.2 16.2 - - + +
524D LEU 2.9 23.0 + - - -
536D PHE* 3.4 7.9 - - - -
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Residues in contact with VAL 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728C GLY 3.7 17.9 - - - +
729C HIS* 3.5 36.2 + - - +
731C TYR* 3.8 30.3 - - + +
734C ALA* 4.1 9.8 - - + +
896C GLY* 4.8 1.8 - - - +
431D VAL* 1.3 90.0 - - + +
433D GLY* 1.3 61.4 + - - +
434D PRO* 4.0 3.8 - - + +
523D GLN* 4.9 3.3 - - - +
524D LEU 4.1 2.0 - - - +
526D PRO* 4.1 15.7 - - + -
536D PHE* 3.3 29.2 - - + -
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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