Contacts of the helix formed by residues 623 - 635 (chain B) in PDB entry 2AN3
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 TRP 623 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B LEU* 3.5 18.6 - - + -
540B TYR* 3.7 37.0 - + + -
582B PRO 3.6 5.8 + - - -
583B THR* 3.3 43.1 - - + -
584B VAL* 3.6 30.5 - - + +
585B TYR* 3.9 20.0 - + + -
588B LEU* 5.9 1.3 - - + -
613B TRP* 3.7 21.6 - + + +
621B PHE* 3.4 34.5 + + - +
622B ASN* 1.3 72.0 + - - +
624B SER* 1.3 62.4 + - - +
625B MET 3.2 2.9 - - - -
626B TYR* 3.1 32.0 + + + +
627B SER* 3.0 22.3 + - - +
644B GLU* 3.7 11.8 + - - +
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Residues in contact with SER 624 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLN* 5.6 1.2 + - - -
622B ASN* 2.6 34.2 + - - -
623B TRP* 1.3 76.8 - - - +
625B MET* 1.3 74.7 + - - +
627B SER* 3.7 3.2 - - - -
628B GLN* 2.8 32.2 + - - +
640B TRP* 4.0 36.1 - - - -
644B GLU* 3.7 10.5 + - - -
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Residues in contact with MET 625 (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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128A GLN* 5.2 4.3 - - - +
140A TRP* 4.0 25.1 - - + +
141A GLN* 3.5 28.7 - - - -
545B GLY 5.0 6.3 - - - +
547B LEU* 3.4 24.1 - - + +
622B ASN* 5.0 8.7 + - - +
623B TRP 3.2 1.0 + - - -
624B SER* 1.3 103.2 + - - +
626B TYR* 1.3 64.8 + - + +
628B GLN* 3.8 4.5 - - - +
629B HIS* 2.9 24.1 + - - +
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Residues in contact with TYR 626 (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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539B ASN 3.8 0.9 + - - -
540B TYR* 3.3 47.0 - + - -
544B ARG 3.8 5.5 + - - -
545B GLY* 3.4 26.8 - - - -
547B LEU* 3.4 32.8 - - + -
554B GLY* 4.6 11.2 - - - -
557B LYS* 5.8 0.7 - - - -
558B LEU* 3.9 15.1 - - + +
585B TYR* 3.8 20.4 - + + -
588B LEU* 3.5 16.5 - - + +
621B PHE* 5.3 1.1 - + - -
622B ASN 5.5 1.1 - - - -
623B TRP* 3.1 33.9 + + + +
625B MET* 1.3 79.1 - - + +
627B SER* 1.3 60.2 + - - +
629B HIS* 3.2 2.3 + - - +
630B ALA* 2.8 30.1 + - - +
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Residues in contact with SER 627 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B LEU* 3.5 22.5 - - - +
613B TRP* 5.4 0.3 - - - -
623B TRP* 3.0 11.8 + - - +
624B SER* 3.7 5.2 - - - -
626B TYR* 1.3 77.9 - - - +
628B GLN* 1.3 61.8 + - - +
630B ALA* 3.2 3.6 + - - +
631B CYS* 3.0 27.5 + - - -
640B TRP* 3.7 18.2 - - - -
643B LYS* 4.5 3.2 - - - +
644B GLU* 2.5 40.3 + - - +
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Residues in contact with GLN 628 (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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128A GLN* 3.2 51.6 + - - +
131A CYS* 4.9 2.8 - - - +
132A LEU* 4.4 13.9 - - - +
138A GLU 5.7 0.2 + - - -
139A CYS* 6.3 0.4 - - - +
140A TRP* 4.3 20.4 - - + +
624B SER 2.8 19.0 + - - +
625B MET* 3.8 4.5 - - + +
627B SER* 1.3 78.3 - - - +
629B HIS* 1.3 57.9 + - - +
631B CYS* 3.2 10.2 + - - +
632B LEU* 2.8 36.0 + - + +
639B CYS* 5.5 0.5 - - - -
640B TRP* 3.7 25.4 + - + +
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Residues in contact with HIS 629 (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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137A GLY 4.5 8.5 - - - -
139A CYS* 5.6 5.5 - - + +
547B LEU* 3.9 32.1 + - + +
550B PRO* 6.2 2.0 - - + -
555B PRO* 3.7 26.2 + - + +
558B LEU* 3.6 27.4 - - + -
559B ARG* 5.0 2.2 + - - -
625B MET 2.9 17.7 + - - +
628B GLN* 1.3 78.0 - - - +
630B ALA* 1.3 57.7 + - - +
632B LEU* 3.2 21.6 + - + +
633B ILE* 2.9 54.4 + - + +
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Residues in contact with ALA 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B LEU* 4.3 8.2 - - + +
588B LEU* 3.8 27.1 - - + -
589B SER* 4.5 5.2 - - - +
626B TYR 2.8 17.2 + - - +
627B SER 3.6 4.9 - - - +
629B HIS* 1.3 77.9 - - - +
631B CYS* 1.3 56.8 + - - +
633B ILE* 3.4 11.5 + - + +
634B GLU* 2.9 47.2 + - - +
643B LYS* 4.5 3.8 - - - -
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Residues in contact with CYS 631 (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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132A LEU* 3.6 8.7 - - + +
627B SER 3.0 17.9 + - - +
628B GLN* 3.2 13.2 + - - +
630B ALA* 1.3 75.3 - - - +
632B LEU* 1.3 64.7 + - - +
634B GLU* 4.1 5.6 - - - +
635B GLY* 3.4 15.6 + - - -
636B LYS 4.3 3.6 + - - -
637B GLY 4.8 1.2 + - - -
638B GLU* 3.2 36.4 + - - +
639B CYS 3.8 1.8 - - - -
640B TRP* 3.7 13.5 - - - -
643B LYS* 3.6 36.3 - - - +
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Residues in contact with LEU 632 (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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131A CYS* 3.6 30.1 - - + +
132A LEU* 3.6 23.4 - - + +
135A GLY* 5.8 2.7 - - - -
137A GLY* 3.4 32.5 - - - +
138A GLU 3.3 23.6 - - - +
139A CYS* 4.7 2.2 - - - +
628B GLN* 2.8 26.5 + - + +
629B HIS* 3.3 25.1 - - + +
630B ALA 3.1 0.2 - - - -
631B CYS* 1.3 79.9 - - - +
633B ILE* 1.3 62.1 + - + +
635B GLY* 3.5 9.7 + - - -
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Residues in contact with ILE 633 (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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137A GLY* 5.7 3.8 - - - -
555B PRO 4.7 0.2 - - - +
558B LEU* 3.6 45.5 - - + +
559B ARG* 3.6 20.2 - - + +
562B ALA* 4.0 13.6 - - + +
589B SER* 5.6 0.2 - - - +
629B HIS* 2.9 43.6 + - + +
630B ALA* 3.6 7.6 - - - +
632B LEU* 1.3 76.3 - - + +
634B GLU* 1.3 67.4 + - - +
635B GLY* 3.1 3.9 + - - -
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Residues in contact with GLU 634 (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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562B ALA* 4.3 12.6 - - + +
588B LEU 4.1 0.3 - - - -
589B SER* 2.8 36.9 + - - +
592B SER* 4.8 2.8 + - - -
630B ALA* 2.9 20.6 + - - +
631B CYS* 4.1 4.9 - - - +
632B LEU 3.4 0.4 - - - -
633B ILE* 1.3 78.0 - - - +
635B GLY* 1.3 63.7 + - - +
636B LYS* 3.5 38.1 + - + +
638B GLU* 4.1 5.7 - - - +
643B LYS* 2.7 37.6 + - - -
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Residues in contact with GLY 635 (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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132A LEU* 6.2 0.4 - - - -
631B CYS 3.4 7.1 + - - -
632B LEU 3.5 8.7 + - - -
633B ILE 3.1 4.7 - - - -
634B GLU* 1.3 81.0 - - - +
636B LYS* 1.3 60.5 + - - +
637B GLY 3.5 2.7 - - - -
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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