Contacts of the strand formed by residues 488 - 496 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B ARG* 5.7 1.8 - - - +
135B ILE* 4.1 15.9 - - + -
153B TRP* 3.6 37.5 - - + +
154B ASN* 3.2 29.4 - - - +
155B PRO* 3.7 2.9 - - + -
156B VAL* 3.6 10.4 - - - +
182B CYS* 3.5 42.8 - - + +
263B ARG* 4.8 4.3 + - - -
484B TRP* 3.7 30.7 - - - +
485B LYS 2.9 16.5 + - - +
486B GLN 3.3 2.2 + - - +
487B TYR* 1.3 85.9 - - - +
489B ARG* 1.3 61.2 + - - +
490B ARG 4.2 0.2 + - - -
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Residues in contact with ARG 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLY 3.9 11.9 + - - -
444A PRO 3.9 13.9 + - - -
446A GLY 4.8 1.4 + - - -
447A SER 3.0 29.0 + - - -
448A ASP* 3.8 28.4 - - - +
449A CYS 4.3 7.0 + - - -
470A GLU* 4.1 14.6 - - + +
152B GLN 3.5 0.9 - - - +
153B TRP* 3.4 7.2 - - - -
154B ASN* 2.8 66.5 + - + +
155B PRO 3.9 14.6 + - - +
156B VAL* 3.9 3.7 - - + +
263B ARG* 3.8 27.8 - - - +
488B MET* 1.3 74.3 - - - +
490B ARG* 1.3 62.8 + - - +
491B SER* 3.8 9.3 + - - -
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Residues in contact with ARG 490 (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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449A CYS 4.2 1.7 - - - +
450A GLY* 3.9 4.0 - - - -
466A ALA* 3.6 25.0 - - - +
470A GLU* 4.1 5.1 + - - +
477A ARG* 2.9 49.1 + - - +
481A SER* 3.1 8.9 + - - -
482A ASP* 2.8 36.0 + - - -
483A SER* 5.1 1.0 - - - +
151B GLU* 2.6 56.8 + - + -
152B GLN 3.5 4.0 - - - -
153B TRP* 3.6 36.8 - - + -
485B LYS* 5.1 1.2 - - - +
489B ARG* 1.3 74.7 - - - +
491B SER* 1.3 66.1 + - - +
492B THR* 4.5 3.6 - - - -
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Residues in contact with SER 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU 4.7 2.1 + - - -
449A CYS 3.7 17.0 - - - -
450A GLY 3.3 4.7 - - - -
452A VAL* 3.8 17.8 - - - +
151B GLU* 3.5 3.6 - - - +
152B GLN* 2.8 59.9 + - - +
154B ASN* 4.5 6.2 + - - -
489B ARG* 3.8 8.2 + - - -
490B ARG* 1.3 77.9 - - - +
492B THR* 1.3 62.0 + - - +
493B CYS* 3.4 9.3 - - - -
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Residues in contact with THR 492 (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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450A GLY 2.8 13.5 + - - -
451A ILE* 3.6 17.5 - - + +
452A VAL 3.2 18.4 + - - -
453A ASN* 4.1 0.2 - - - +
461A ALA* 6.6 0.2 - - + -
462A GLU 5.9 0.4 - - - +
465A GLY* 4.0 17.7 - - - -
466A ALA* 2.6 38.6 + - - +
477A ARG* 5.3 0.5 + - - -
140B LEU* 5.5 2.5 - - + -
149B LEU* 3.8 21.8 - - + -
150B ILE 3.9 3.1 - - - +
151B GLU* 4.8 5.6 - - + +
490B ARG* 4.4 5.0 - - - +
491B SER* 1.3 70.5 - - - +
493B CYS* 1.3 61.9 + - - +
494B THR* 4.1 2.3 + - - +
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Residues in contact with CYS 493 (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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442A LEU* 4.0 19.5 - - + -
452A VAL* 3.3 21.3 - - - +
148B ALA 3.7 0.7 - - - +
149B LEU* 3.3 6.4 - - - +
150B ILE* 2.8 54.1 + - + +
152B GLN* 3.9 17.3 - - - -
491B SER* 3.4 34.1 - - - -
492B THR* 1.3 74.2 - - - +
494B THR* 1.3 62.3 + - - +
495B ILE* 4.1 2.7 + - + +
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Residues in contact with THR 494 (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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452A VAL 3.8 0.8 + - - -
453A ASN* 3.2 24.9 + - - -
454A VAL 3.0 24.6 + - - -
456A ILE* 3.7 16.8 - - + +
460A GLY 4.4 7.9 + - - +
461A ALA* 5.4 2.8 - - - -
462A GLU* 4.7 8.3 + - - +
142B SER* 5.2 0.7 - - - +
144B ARG* 4.6 8.2 + - - +
147B HIS* 3.8 29.8 - - + -
148B ALA 3.3 9.0 - - - +
149B LEU* 3.4 18.3 - - + +
492B THR* 4.1 1.4 + - - +
493B CYS* 1.3 71.4 + - - +
495B ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 495 (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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438A VAL* 4.4 12.3 - - + -
439A PHE* 5.3 3.8 - - + -
442A LEU* 3.7 31.0 - - + -
454A VAL* 3.8 27.8 - - + -
147B HIS* 3.3 3.8 - - - -
148B ALA* 2.7 50.8 + - + +
150B ILE* 4.9 12.1 - - + -
493B CYS 4.8 3.4 - - - +
494B THR* 1.3 79.7 - - - +
496B ASN* 1.3 66.7 + - - +
497B TYR* 3.6 4.4 + - + +
435D LEU* 4.7 7.2 - - + -
439D PHE* 4.1 32.8 - - + -
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Residues in contact with ASN 496 (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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284A LEU* 3.8 17.2 - - - +
454A VAL 3.0 10.0 + - - +
455A ASN* 2.8 60.5 + - - +
456A ILE* 4.4 2.4 - - + +
146B GLY 3.8 1.5 - - - +
147B HIS* 3.5 35.0 - - + +
494B THR 4.0 1.0 - - - -
495B ILE* 1.3 71.7 - - - +
497B TYR* 1.3 59.2 + - - +
498B SER* 2.9 35.8 + - - +
500B ASP 4.8 4.4 + - - +
435D LEU* 4.1 3.1 - - - +
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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