Contacts of the helix formed by residues 617 - 635 (chain A) in PDB entry 3S95
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 LEU 617 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A PRO* 3.8 33.7 - - + +
578A SER* 4.5 4.5 - - - +
606A THR* 3.2 18.3 - - - +
607A LEU* 3.8 22.4 - - + +
610A HIS* 3.7 45.1 + - + +
615A LEU 3.5 0.8 + - - -
616A PRO* 1.3 73.5 - - - +
618A GLY* 1.3 65.8 + - - +
621A LEU* 3.6 38.7 + - + +
622A GLU* 5.2 4.3 - - + +
557B MET* 4.5 6.0 - - + +
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Residues in contact with GLY 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A THR* 5.3 0.7 - - - -
616A PRO* 3.2 6.3 - - - -
617A LEU* 1.3 81.9 - - - +
619A PRO* 1.3 75.5 - - - +
620A GLN 3.4 2.6 + - - -
622A GLU* 3.1 22.9 + - - +
639A CL 4.2 5.6 - - - -
557B MET* 3.3 19.3 - - - +
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Residues in contact with PRO 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GOL 3.6 20.9 - - - +
618A GLY* 1.3 82.4 - - - +
620A GLN* 1.3 66.3 + - - +
622A GLU* 3.7 6.2 - - + +
623A GLN* 2.9 28.8 + - - +
639A CL 3.5 14.8 - - + -
555B ARG* 4.1 19.5 - - + +
556B THR 3.4 30.5 - - - +
557B MET* 4.3 7.6 - - + -
559B PHE* 3.6 22.7 - - + -
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Residues in contact with GLN 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GOL 3.4 22.9 - - - +
599A LYS* 2.7 26.0 + - - +
603A TRP* 3.0 30.7 + - + +
618A GLY 3.4 1.0 - - - -
619A PRO* 1.3 77.6 - - - +
621A LEU* 1.3 59.4 + - + +
623A GLN* 3.8 3.4 - - - +
624A LEU* 3.0 27.7 + - - +
639A CL 3.3 22.4 - - + +
514B TYR* 4.8 4.4 + - + -
550B PRO* 3.5 22.2 - - + +
551B ASP* 2.8 26.8 + - - +
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Residues in contact with LEU 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A SER* 3.7 25.0 - - - +
582A ILE* 4.0 14.1 - - + -
603A TRP* 3.6 62.1 - - + +
606A THR* 4.1 7.0 - - + -
607A LEU* 4.4 2.9 - - + +
617A LEU* 3.6 42.8 + - + +
618A GLY 3.5 2.4 + - - -
619A PRO 3.3 0.2 - - - -
620A GLN* 1.3 76.0 - - + +
622A GLU* 1.3 60.8 + - - +
624A LEU* 3.7 13.2 - - + +
625A ASP* 2.9 31.4 + - - +
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Residues in contact with GLU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LEU* 5.2 4.9 - - + +
618A GLY 3.1 18.2 + - - +
619A PRO* 3.7 4.3 - - + +
621A LEU* 1.3 77.8 - - - +
623A GLN* 1.3 59.2 + - - +
625A ASP* 3.8 3.7 - - - +
626A ARG* 3.0 55.7 + - + +
557B MET* 2.8 44.2 - - + +
559B PHE* 4.3 13.9 - - - -
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Residues in contact with GLN 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GOL 4.2 14.1 + - - +
619A PRO 2.9 20.5 + - - +
620A GLN* 3.8 4.5 - - - +
622A GLU* 1.3 79.7 + - + +
624A LEU* 1.3 57.5 + - - +
626A ARG* 3.1 31.1 + - - +
627A GLY* 2.8 29.1 + - - -
521B ILE* 3.6 18.9 + - - +
522B ASN* 5.3 1.8 + - - -
559B PHE* 3.4 35.8 - - + -
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GOL 4.8 2.9 - - - +
578A SER* 4.3 2.7 - - - +
581A PRO* 3.9 9.9 - - + +
582A ILE* 3.5 44.9 - - + +
585A ARG* 4.2 27.4 - - + -
603A TRP* 3.9 26.5 - - + -
620A GLN 3.0 18.3 + - - +
621A LEU* 3.7 13.5 - - + +
623A GLN* 1.3 75.3 - - - +
625A ASP* 1.3 63.0 + - - +
627A GLY* 4.0 0.4 - - - -
628A PHE* 3.0 25.0 + - + +
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Residues in contact with ASP 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A PRO* 4.0 10.0 - - + +
578A SER* 2.9 33.2 + - - +
581A PRO* 3.4 17.7 - - - +
621A LEU 2.9 18.1 + - - +
622A GLU* 3.8 4.7 - - - +
624A LEU* 1.3 77.6 - - - +
626A ARG* 1.3 67.3 + - + +
628A PHE* 3.3 2.1 + - - +
629A TRP* 3.1 46.6 + - - -
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Residues in contact with ARG 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A GLU* 3.0 40.9 + - + +
623A GLN* 3.1 29.9 - - - +
625A ASP* 1.3 80.6 - - + +
627A GLY* 1.3 57.1 + - - +
629A TRP* 3.3 5.2 + - - +
630A GLU* 2.9 34.9 + - - +
633A ARG* 5.3 0.5 + - - -
522B ASN* 6.0 0.2 + - - -
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Residues in contact with GLY 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A GLN 2.8 18.6 + - - -
624A LEU 4.0 0.7 - - - -
626A ARG* 1.3 73.2 - - - +
628A PHE* 1.3 66.6 + - - +
630A GLU* 4.0 7.1 - - - +
631A THR* 2.9 30.8 + - - -
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Residues in contact with PHE 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A VAL* 3.7 26.2 - - + -
567A LEU* 4.5 0.9 - - + -
580A PHE* 3.9 12.8 - + - -
581A PRO* 3.8 19.7 - - + -
584A VAL* 3.8 35.9 - - + -
624A LEU* 3.0 18.6 + - + +
625A ASP 3.7 3.4 - - - +
627A GLY* 1.3 77.0 - - - +
629A TRP* 1.3 104.6 - + - +
631A THR* 3.3 3.9 + - - -
632A TYR* 2.8 38.9 + + + +
637A SER* 4.2 12.3 - - - -
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Residues in contact with TRP 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU* 3.9 28.3 - - + -
580A PHE* 4.9 5.8 - + + -
581A PRO* 4.3 4.2 - - + +
625A ASP* 3.1 48.3 + - - +
626A ARG* 4.1 4.0 - - - +
628A PHE* 1.3 103.9 - + - +
630A GLU* 1.3 57.2 + - - +
632A TYR* 3.7 30.4 - + - +
633A ARG* 2.9 42.8 + - + +
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Residues in contact with GLU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A ARG* 2.9 21.4 + - - +
627A GLY* 4.0 6.5 - - - +
629A TRP* 1.3 74.9 - - - +
631A THR* 1.3 69.0 + - - +
633A ARG* 3.3 30.0 + - - +
634A ARG* 3.1 64.1 + - - +
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Residues in contact with THR 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627A GLY 2.9 19.7 + - - -
628A PHE* 3.7 4.7 - - - -
630A GLU* 1.3 75.7 + - - +
632A TYR* 1.3 66.5 + - - +
634A ARG* 3.2 15.7 + - - +
636A GLU* 3.2 46.2 + - + +
637A SER* 3.8 11.9 - - - +
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Residues in contact with TYR 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563A VAL* 3.9 22.2 - - + -
564A ARG* 3.4 63.2 + - + +
567A LEU* 3.5 24.6 - - + +
568A ASP* 5.2 1.7 + - - -
628A PHE* 2.8 35.8 + + + +
629A TRP* 3.7 23.6 - + + +
631A THR* 1.3 73.4 - - - +
633A ARG* 1.3 64.1 + - + +
635A GLY* 3.1 15.6 + - - -
637A SER* 3.6 21.8 + - - +
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Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A ARG 5.3 0.2 + - - -
629A TRP* 2.9 21.0 + - + +
630A GLU* 3.3 55.8 + - - +
632A TYR* 1.3 81.3 - - + +
634A ARG* 1.3 74.4 + - + +
635A GLY* 3.1 2.0 + - - -
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Residues in contact with ARG 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630A GLU* 3.1 56.0 + - - +
631A THR* 3.2 10.0 + - - +
633A ARG* 1.3 87.7 - - + +
635A GLY* 1.3 58.1 + - - +
636A GLU* 3.5 22.5 - - + +
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Residues in contact with GLY 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A ARG* 4.8 11.8 + - - -
632A TYR 3.1 10.0 + - - -
633A ARG 3.1 5.9 - - - -
634A ARG* 1.3 79.2 - - - +
636A GLU* 1.3 59.7 + - - +
637A SER 3.4 7.3 + - - -
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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
------------------------------------------------------------
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