Contacts of the strand formed by residues 627 - 632 (chain D) in PDB entry 1JZ3
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 PHE 627 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625D GLN* 4.0 12.4 + - - +
626D PHE* 1.4 86.7 - - + +
628D GLN* 1.3 69.8 + - - +
629D PHE* 3.6 32.1 - - + -
638D VAL* 4.0 21.3 - - + -
639D THR 3.3 2.0 - - - +
640D SER* 4.0 19.5 - - - -
642D TYR* 3.8 28.0 - + - -
647D SER* 4.1 13.5 - - - -
650D GLU* 4.0 27.6 - - + -
670D LEU* 4.0 5.4 - - + -
672D VAL* 3.8 22.9 - - + -
700D VAL* 4.2 19.1 - - + -
715D SER* 4.7 6.1 - - - -
716D ALA* 4.7 6.7 - - + -
8402D DMS 4.4 0.2 + - - -
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Residues in contact with GLN 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D ARG* 3.2 31.8 + - - +
625D GLN 3.7 1.9 - - - +
627D PHE* 1.3 80.3 - - - +
629D PHE* 1.3 65.0 + - - +
630D ARG* 4.4 18.6 - - - +
638D VAL* 3.5 4.9 - - - +
639D THR* 2.8 45.2 + - + +
641D GLU* 3.2 28.4 - - + +
8402D DMS 2.8 43.6 + - - +
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Residues in contact with PHE 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625D GLN* 4.3 12.8 - - - -
627D PHE* 3.6 22.7 - - + -
628D GLN* 1.3 82.1 - - - +
630D ARG* 1.3 83.6 + - - +
636D ILE* 4.2 10.1 - - + -
637D GLU 3.2 5.2 - - - -
638D VAL* 4.0 26.9 - - + -
652D LEU* 3.7 24.0 - - + -
698D VAL* 4.2 9.0 - - + -
700D VAL* 3.8 24.0 - - + -
716D ALA* 4.4 4.5 - - + -
717D TRP 4.4 5.2 - - - -
718D GLN* 3.8 26.7 - - + -
720D TRP* 3.6 21.3 - + + -
8503D DMS 3.5 13.5 + - - +
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Residues in contact with ARG 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628D GLN* 4.4 18.2 - - - +
629D PHE* 1.3 104.9 + - - +
631D LEU* 1.3 60.1 + - - +
635D THR 3.7 0.5 - - - +
636D ILE* 3.4 4.2 - - - +
637D GLU* 2.8 59.6 + - + +
720D TRP* 4.2 3.6 - - - -
8503D DMS 3.8 25.2 - - - +
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Residues in contact with LEU 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630D ARG* 1.3 77.4 - - - +
632D SER* 1.3 63.2 + - - +
633D GLY 3.7 20.0 - - - +
634D GLN* 4.5 2.0 - - - -
635D THR 3.4 21.3 - - - +
636D ILE* 4.0 13.7 - - + -
682D LEU* 6.1 0.7 - - + -
696D LEU* 4.3 8.7 - - + -
720D TRP* 3.7 44.4 - - + +
721D ARG 5.1 1.6 - - - +
722D LEU* 3.7 28.9 - - + -
8503D DMS 4.4 1.2 + - - -
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Residues in contact with SER 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630D ARG 4.3 0.2 - - - -
631D LEU* 1.3 74.5 + - - +
633D GLY* 1.3 61.2 + - - +
634D GLN 3.0 0.9 + - - -
635D THR* 2.9 41.0 + - - -
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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