Contacts of the strand formed by residues 422 - 429 (chain B) in PDB entry 4L1O
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 422 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 4.6 3.6 - - - -
102B GLU 3.2 19.8 + - - -
104B LEU* 3.8 11.5 - - - +
130B ALA* 3.4 14.9 + - - +
418B PHE* 2.6 39.9 + - - -
419B GLU* 3.0 17.8 + - - +
420B THR 3.9 3.8 - - - +
421B PHE* 1.3 79.7 - - - +
423B HIS* 1.3 65.3 + - - +
424B ARG* 4.0 3.2 + - - -
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Residues in contact with HIS 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A SER* 5.0 0.9 - - - +
382A SER 2.8 30.6 + - - -
383A GLY* 3.1 21.4 + - - -
402A GLY 4.7 1.8 + - - -
403A GLY 3.5 17.3 + - - -
404A VAL* 3.7 23.4 - - + +
100B HIS 3.5 5.2 - - - +
101B SER* 3.6 0.7 - - - -
102B GLU* 2.8 53.7 + - + +
103B PRO 5.1 1.1 - - - +
104B LEU* 3.7 18.0 - - + +
422B SER* 1.3 74.1 - - - +
424B ARG* 1.3 73.1 + - - +
425B ARG* 3.6 12.2 + - + +
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Residues in contact with ARG 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLY 4.4 1.0 - - - +
400A PRO* 5.7 3.6 - - - +
416A LYS* 6.3 1.6 - - - +
80B TRP 5.9 0.4 + - - -
84B GLU* 3.5 26.7 + - - -
99B ILE* 3.6 36.0 - - + +
100B HIS 3.7 3.8 - - - -
101B SER* 4.2 19.4 + - - +
415B LYS* 4.5 5.9 - - - +
418B PHE* 6.2 1.2 - - - -
419B GLU* 4.0 52.3 + - + +
422B SER* 4.0 2.8 + - - -
423B HIS* 1.3 86.0 + - - +
425B ARG* 1.3 59.1 + - - +
426B SER* 3.9 3.6 + - - -
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 3.5 9.9 - - - +
377A ILE* 2.9 31.9 + - - +
380A THR* 3.0 25.5 + - - -
382A SER* 2.9 50.0 + - - +
383A GLY 3.7 11.9 - - - +
384A GLY* 4.2 4.5 - - - -
385A VAL* 3.1 22.8 - - + +
99B ILE* 3.5 4.0 - - - +
100B HIS* 2.7 48.5 + - + +
102B GLU* 2.8 33.4 + - - +
423B HIS* 3.7 8.7 - - + +
424B ARG* 1.3 71.0 - - - +
426B SER* 1.3 65.9 + - - +
427B CYS* 3.5 7.2 + - - -
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLY 3.9 5.6 + - - -
384A GLY* 3.2 7.0 - - - -
385A VAL 2.8 32.4 + - - +
393A HIS* 4.7 6.2 + - - -
399A LEU* 3.5 22.7 - - - +
400A PRO* 2.6 47.9 + - - +
98B TYR 3.8 4.0 - - - -
99B ILE* 4.6 4.3 - - - +
424B ARG 3.9 3.9 + - - -
425B ARG* 1.3 71.9 - - - +
427B CYS* 1.3 54.1 + - - +
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Residues in contact with CYS 427 (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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377A ILE* 4.6 7.4 - - + -
385A VAL* 3.4 24.7 - - + +
399A LEU* 4.0 6.5 - - - +
96B GLU 3.8 1.1 - - - +
97B LEU* 3.4 5.9 - - - -
98B TYR* 2.8 73.9 + - + +
100B HIS* 3.7 10.3 - - - -
425B ARG* 3.5 18.6 - - - -
426B SER* 1.3 75.3 - - - +
428B LEU* 1.3 59.9 + - - +
429B VAL* 4.9 4.0 - - + -
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Residues in contact with LEU 428 (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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385A VAL* 2.9 9.9 + - - +
386A ALA* 3.1 6.3 - - + +
387A ALA 2.7 31.9 + - - +
392A VAL* 3.3 35.7 - - + -
393A HIS* 3.8 25.6 - - + +
396A LEU* 4.2 11.2 - - + -
399A LEU* 4.3 6.9 - - + +
92B THR* 4.9 2.5 - - + -
95B ASP* 3.7 20.6 - - + +
96B GLU 3.7 0.7 - - - -
97B LEU* 3.3 30.1 - - + -
427B CYS* 1.3 72.5 - - - +
429B VAL* 1.3 57.8 + - - +
430B ARG* 4.0 15.7 - - + +
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Residues in contact with VAL 429 (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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373A ILE* 4.4 22.0 - - + -
377A ILE* 4.8 4.7 - - + -
385A VAL* 5.8 0.7 - - + -
387A ALA* 4.0 21.3 - - + +
95B ASP* 3.6 3.9 - - - +
96B GLU* 3.0 42.8 + - + +
98B TYR* 3.9 32.3 - - + +
427B CYS* 4.9 1.1 - - + -
428B LEU* 1.3 78.1 - - - +
430B ARG* 1.3 66.1 + - - +
431B PRO* 4.4 0.7 - - - +
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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