Contacts of the strand formed by residues 488 - 496 (chain C) in PDB entry 2JG7
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 MET 488 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C ARG* 5.6 2.0 - - - +
135C ILE* 4.1 14.6 - - + -
153C TRP* 3.6 37.8 - - + +
154C ASN* 3.2 31.9 - - - +
155C PRO* 3.7 2.7 - - + -
156C VAL* 3.5 12.0 - - - +
182C CYS* 3.5 44.4 - - + +
263C ARG* 4.8 4.3 + - - -
484C TRP* 3.6 30.7 - - + +
485C LYS 2.9 16.1 + - - +
486C GLN 3.3 2.0 + - - +
487C TYR* 1.3 86.9 - - - +
489C ARG* 1.3 59.6 + - - +
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Residues in contact with ARG 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLN 3.5 0.7 - - - +
153C TRP* 3.4 7.5 - - - -
154C ASN* 2.8 66.9 + - - +
155C PRO 3.9 14.4 + - - +
156C VAL* 3.9 2.4 + - + +
263C ARG* 3.8 28.0 - - - +
488C MET* 1.3 74.1 - - - +
490C ARG* 1.3 60.7 + - - +
491C SER* 4.7 9.5 + - - -
443D GLY 3.9 6.9 + - - -
444D PRO 3.9 18.4 + - - -
446D GLY 4.8 1.6 + - - -
447D SER 3.1 29.4 + - - -
448D ASP* 3.9 29.0 - - - +
449D CYS 4.3 7.8 + - - -
452D VAL* 5.4 0.2 - - - +
470D GLU* 4.1 14.6 - - + -
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Residues in contact with ARG 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU* 2.6 53.7 + - + -
152C GLN 3.5 4.0 - - - -
153C TRP* 3.6 37.3 - - + -
485C LYS* 5.0 2.2 - - - +
489C ARG* 1.3 74.7 - - - +
491C SER* 1.3 65.2 + - - +
492C THR* 4.5 3.4 - - - -
449D CYS 4.1 1.9 - - - +
450D GLY* 3.9 4.5 - - - -
466D ALA* 3.6 26.4 - - - +
470D GLU* 4.1 5.5 + - - +
477D ARG* 3.0 49.1 + - - +
481D SER* 3.2 8.3 + - - -
482D ASP* 2.8 35.6 + - - -
483D SER* 5.2 1.4 - - - +
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Residues in contact with SER 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU* 3.5 3.5 - - - +
152C GLN* 2.8 59.8 + - - +
154C ASN* 4.5 6.4 + - - -
489C ARG* 4.7 7.4 + - - -
490C ARG* 1.3 78.9 - - - +
492C THR* 1.3 60.8 + - - +
493C CYS* 3.4 9.0 - - - -
442D LEU 4.7 2.4 + - - -
449D CYS 3.6 17.5 - - - -
450D GLY 3.3 4.5 - - - -
452D VAL* 3.8 18.4 - - - +
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Residues in contact with THR 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LEU* 5.5 2.9 - - + -
149C LEU* 3.9 21.3 - - + -
150C ILE 3.9 3.4 - - - +
151C GLU* 4.8 6.1 - - + +
490C ARG* 4.5 5.0 - - - +
491C SER* 1.3 69.6 - - - +
493C CYS* 1.3 61.3 + - - +
494C THR* 4.1 1.6 + - - +
450D GLY 2.8 13.1 + - - -
451D ILE* 3.6 17.2 - - + +
452D VAL 3.2 18.2 + - - -
453D ASN* 4.1 1.0 - - - +
461D ALA* 6.6 0.2 - - + -
462D GLU 5.9 0.9 - - - +
465D GLY* 3.9 17.7 - - - -
466D ALA* 2.6 38.7 + - - +
477D ARG* 5.3 0.7 + - - -
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Residues in contact with CYS 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ALA 3.7 1.2 - - - +
149C LEU* 3.3 5.7 - - - +
150C ILE* 2.8 54.2 + - + +
152C GLN* 4.0 12.3 - - - -
491C SER* 3.4 31.9 - - - -
492C THR* 1.3 74.6 - - - +
494C THR* 1.3 62.2 + - - +
495C ILE* 4.1 2.3 + - + +
442D LEU* 4.0 20.9 - - + -
452D VAL* 3.3 26.9 - - - +
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Residues in contact with THR 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C SER* 5.1 0.7 - - - +
144C ARG* 4.7 8.6 + - - +
147C HIS* 3.9 29.6 - - + -
148C ALA 3.4 9.0 - - - +
149C LEU* 3.4 17.9 - - + +
492C THR* 5.1 1.7 + - - +
493C CYS* 1.3 71.1 - - - +
495C ILE* 1.3 63.3 + - - +
452D VAL 3.8 0.6 + - - -
453D ASN* 3.2 22.7 + - - -
454D VAL 3.0 24.4 + - - -
456D ILE* 3.7 17.4 - - + +
460D GLY 4.4 8.8 + - - +
461D ALA* 5.4 2.9 - - - -
462D GLU* 4.7 8.1 + - - +
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Residues in contact with ILE 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A LEU* 4.7 6.7 - - + -
439A PHE* 4.1 31.9 - - + -
147C HIS* 3.2 4.0 - - - -
148C ALA* 2.7 50.2 + - + +
150C ILE* 4.9 13.0 - - + -
493C CYS 4.8 3.1 - - - +
494C THR* 1.3 79.8 - - - +
496C ASN* 1.3 67.5 + - - +
497C TYR* 3.6 4.2 + - + +
438D VAL* 4.4 13.5 - - + -
439D PHE* 5.3 3.4 - - + -
442D LEU* 3.7 30.5 - - + -
454D VAL* 3.9 28.3 - - + -
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Residues in contact with ASN 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A LEU* 4.1 2.9 - - - +
146C GLY 3.9 3.6 - - - -
147C HIS* 3.5 30.5 - - + +
494C THR 4.0 1.0 - - - -
495C ILE* 1.3 71.4 - - - +
497C TYR* 1.3 59.6 + - - +
498C SER* 2.9 34.8 + - - +
500C ASP 4.8 4.6 + - - -
284D LEU* 3.9 16.6 - - - +
454D VAL 3.1 9.8 + - - +
455D ASN* 2.9 58.1 + - - +
456D ILE* 4.5 3.3 - - + +
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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