Contacts of the strand formed by residues 426 - 434 (chain K) in PDB entry 6T9L
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 426 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D THR* 3.3 19.0 - - - +
235K GLN* 4.3 0.2 + - - -
419K HIS* 3.5 9.0 - - - -
420K LYS 3.2 12.8 - - - -
421K GLY* 3.7 2.5 - - - -
425K GLU* 1.3 81.4 - - - +
427K HIS* 1.3 60.3 + - - +
74O ARG 3.6 5.3 + - - -
75O GLY* 3.8 6.6 - - - -
76O GLY 2.8 20.1 + - - -
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Residues in contact with HIS 427 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D THR* 5.5 2.0 - - + -
117D LYS* 3.8 8.3 + - - -
120D SER* 5.1 17.0 - - - -
146K CYS* 2.9 41.6 - - + +
418K SER 4.1 0.2 - - - +
419K HIS* 3.3 8.8 + - - -
420K LYS* 2.8 37.4 + - + +
426K GLY* 1.3 73.9 - - - +
428K TYR* 1.3 79.3 + - - +
429K ILE* 3.6 20.4 - - + +
443K ASN* 3.4 17.6 + - - -
444K ASP* 3.1 11.0 - - - -
76O GLY 3.3 9.0 + - - +
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Residues in contact with TYR 428 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K CYS* 3.6 22.0 - - - +
147K PHE* 3.6 30.1 - - + -
150K SER* 4.4 9.6 - - - +
236K GLN 4.2 1.3 - - - -
237K ASP* 3.7 2.9 + - - -
238K ALA* 3.5 27.4 + - + +
417K VAL* 4.5 12.1 - - + -
418K SER 3.6 3.8 - - - -
419K HIS* 3.3 39.5 - + + -
427K HIS* 1.3 94.2 + - - +
429K ILE* 1.3 61.0 + - - +
442K PHE 5.4 0.2 - - - +
443K ASN* 4.4 1.9 - - - +
444K ASP* 4.8 2.9 - - - +
461K TYR* 4.5 12.9 - + - -
73O LEU* 2.3 35.8 + - - +
75O GLY* 3.6 24.7 - - - -
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Residues in contact with ILE 429 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K SER* 5.2 0.7 - - - -
417K VAL* 4.9 1.8 - - - -
418K SER* 2.6 51.5 + - - +
420K LYS* 6.6 0.2 - - + -
427K HIS* 3.6 16.1 + - + -
428K TYR* 1.3 79.2 - - - +
430K ALA* 1.3 62.1 + - - +
431K PHE* 3.8 32.7 - - + -
441K LYS* 4.6 19.1 - - + +
442K PHE 4.3 8.7 - - - +
443K ASN* 3.5 24.5 - - - +
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Residues in contact with ALA 430 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K SER* 3.9 35.2 - - - +
153K GLN* 5.1 3.4 - - + -
154K CYS* 6.1 1.6 - - + +
416K ILE 3.5 7.6 - - - +
417K VAL* 4.2 11.9 - - + +
429K ILE* 1.3 73.3 - - - +
431K PHE* 1.3 67.8 + - - +
432K CYS* 6.1 0.7 - - + -
442K PHE* 3.0 45.3 + - + +
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Residues in contact with PHE 431 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415K GLY* 3.5 1.0 - - - -
416K ILE* 2.5 65.3 + - + +
418K SER* 4.1 15.5 - - - -
429K ILE* 3.8 16.8 - - + -
430K ALA* 1.3 80.3 - - - +
432K CYS* 1.3 60.4 + - - +
439K TRP* 3.7 6.5 - - + -
440K PHE 3.5 17.3 - - - +
441K LYS* 3.6 33.0 - - + -
450K ILE* 4.7 13.0 - - + -
455K VAL* 4.0 28.3 - - + -
458K GLU* 3.7 32.5 - - + -
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Residues in contact with CYS 432 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K GLN* 5.9 0.2 - - + -
154K CYS* 4.8 19.1 - - + -
157K HIS* 3.7 32.5 - - - -
414K ILE 3.8 11.4 - - - +
415K GLY* 4.5 2.2 - - - -
430K ALA* 4.2 2.1 - - + -
431K PHE* 1.3 74.1 - - - +
433K LYS* 1.3 75.5 + - - +
434K ILE* 4.3 1.4 + - - +
439K TRP* 3.5 6.8 - - - -
440K PHE* 3.3 32.9 + - - +
442K PHE* 3.6 23.4 - - + -
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Residues in contact with LYS 433 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K HIS* 4.8 4.7 - - - +
384K THR* 6.0 3.4 - - - -
385K TYR* 5.8 1.2 + - - -
412K GLU* 3.0 24.7 + - - +
413K LEU 3.2 23.4 + - - -
414K ILE* 3.2 14.8 + - - +
432K CYS* 1.3 87.0 - - - +
434K ILE* 1.3 73.1 + - - +
437K GLY* 4.1 17.0 - - - -
438K GLN 3.7 14.8 - - - +
439K TRP* 3.4 41.0 - - + +
452K GLN* 5.3 7.1 - - - +
69N LEU* 3.8 27.1 - - - +
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Residues in contact with ILE 434 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K ASP* 4.2 27.6 - - + +
136K LEU* 4.9 2.9 - - + -
157K HIS* 3.7 37.2 - - + +
432K CYS* 4.8 2.2 - - - +
433K LYS* 1.3 88.3 - - - +
435K SER* 1.3 75.7 + - - +
437K GLY 3.4 12.6 + - - -
438K GLN* 3.3 17.6 + - + +
440K PHE* 3.6 33.4 - - + -
442K PHE* 5.2 1.1 - - + -
48M TYR* 5.8 1.3 - - + -
69N LEU* 3.7 9.6 - - - +
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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