Contacts of the strand formed by residues 415 - 425 (chain B) in PDB entry 1T94
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 415 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413B ARG* 3.5 11.6 + - - +
414B LYS* 1.3 85.2 - - - +
416B MET* 1.3 70.1 + - - +
417B SER 4.1 0.9 + - - -
512B ARG* 3.0 35.0 + - - -
513B ILE 3.2 11.9 - - - -
514B SER* 4.1 5.4 - - - -
516B PHE* 3.2 16.8 - - - -
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ARG* 3.2 14.6 - - - +
413B ARG* 2.6 56.8 - - + +
415B SER* 1.3 70.8 - - - +
417B SER* 1.3 60.7 + - - +
442B LEU* 3.5 14.5 - - + +
445B ASP* 4.0 25.8 - - - +
446B LEU* 4.1 11.9 - - + -
449B GLU* 5.0 4.7 - - - +
451B LEU* 4.3 10.8 - - + -
512B ARG* 3.1 4.3 - - - +
513B ILE* 2.7 60.9 + - + -
516B PHE* 3.6 14.1 - - + -
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Residues in contact with SER 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN* 4.4 6.2 + - - +
409B ARG* 3.4 21.3 + - - +
413B ARG* 5.4 0.2 - - - +
415B SER 4.1 1.0 + - - -
416B MET* 1.3 72.6 - - - +
418B VAL* 1.3 71.2 + - - +
419B GLU* 3.9 16.5 + - - +
442B LEU* 3.8 0.6 - - - +
511B VAL 3.6 7.4 + - - -
512B ARG* 2.9 42.5 + - - +
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Residues in contact with VAL 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN* 3.8 7.6 - - - +
409B ARG* 4.3 9.9 - - - +
417B SER* 1.3 82.8 + - - +
419B GLU* 1.3 65.9 - - - +
438B LEU* 3.5 31.5 - - + +
441B GLU* 3.3 47.3 - - - +
442B LEU* 3.4 20.9 - - + -
445B ASP* 4.8 0.4 - - - +
510B GLY* 3.4 1.7 - - - -
511B VAL 3.0 32.1 + - - +
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PRO* 4.0 25.9 - - + +
191B ASN* 2.8 34.2 + - - +
417B SER* 3.9 15.4 + - - +
418B VAL* 1.3 83.7 - - - +
420B ARG* 1.3 66.4 + - - +
438B LEU* 4.3 2.9 - - - +
441B GLU* 5.5 0.5 - - - +
459B LYS* 3.0 41.9 + - - +
508B LEU* 4.0 11.0 - - + +
509B MET 3.5 5.2 - - - +
510B GLY* 3.6 15.5 - - - +
512B ARG* 4.6 8.1 + - - -
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Residues in contact with ARG 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PRO* 4.1 4.5 - - + -
210B GLU* 6.1 0.9 - - - +
419B GLU* 1.3 78.4 + - - +
421B THR* 1.3 66.4 + - - +
422B PHE* 3.1 26.5 - - + -
434B LEU* 3.5 28.0 - - + +
437B GLU* 3.5 38.4 + - - +
438B LEU* 4.2 15.8 - - + +
441B GLU* 3.3 30.3 + - - -
508B LEU* 2.6 23.0 - - - +
509B MET 3.1 9.6 + - - +
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Residues in contact with THR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ALA 4.4 4.0 - - - +
187B ASP* 3.7 29.7 + - - +
188B TYR 5.8 0.2 - - - -
190B PRO* 3.5 25.7 - - + +
210B GLU* 4.7 9.9 - - - +
420B ARG* 1.3 83.1 - - - +
422B PHE* 1.3 68.6 + - - +
461B LYS* 6.0 0.2 + - - -
507B ARG* 3.2 18.7 + - - +
508B LEU* 3.9 8.3 - - - +
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Residues in contact with PHE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLU* 5.5 7.0 - - - +
420B ARG* 3.1 31.2 - - + -
421B THR* 1.3 84.5 + - - +
423B SER* 1.3 71.8 + - - +
425B ILE* 3.3 31.0 - - + -
431B GLN* 6.5 0.4 - - + -
434B LEU* 3.3 34.5 - - + -
506B LEU* 3.1 29.2 - - + -
507B ARG* 3.1 34.9 + - - +
508B LEU* 3.4 21.3 - - - -
509B MET* 3.8 3.8 - - + -
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B LYS* 4.8 18.5 + - - -
422B PHE* 1.3 77.9 - - - +
424B GLU* 1.3 73.8 + - - +
425B ILE* 3.3 12.3 + - - +
507B ARG* 3.5 13.2 - - - +
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B PHE 3.7 2.0 + - - -
423B SER* 1.3 83.1 + - - +
425B ILE* 1.3 62.5 + - - +
426B ASN* 2.3 37.9 + - - +
463B VAL* 3.5 31.6 - - + +
505B ARG* 3.0 31.2 + - + -
506B LEU 3.4 8.7 - - - -
507B ARG* 3.7 9.4 - - - +
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B PHE* 3.3 39.9 - - + -
423B SER 3.4 13.7 - - - +
424B GLU* 1.3 74.8 - - - +
426B ASN* 1.3 55.9 + - - +
427B LYS 4.2 2.0 - - - +
430B GLU* 3.9 41.5 - - + +
431B GLN* 2.8 37.9 + - + +
434B LEU* 4.4 11.0 - - + -
504B LEU 3.0 8.7 - - - +
506B LEU* 3.1 16.6 + - + +
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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