Contacts of the helix formed by residues 627 - 638 (chain A) in PDB entry 1IS2
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 ASN 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 4.4 5.9 - - - -
2A ASN* 3.8 22.8 - - - +
623A ARG* 3.6 6.2 - - - +
625A ASP* 3.0 33.7 + - - +
626A GLY* 1.3 73.3 - - - +
628A VAL* 1.3 61.5 + - - +
629A TYR 3.8 0.9 - - - -
630A GLU* 5.0 15.2 + - - +
631A ASN* 2.6 41.7 + - - +
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Residues in contact with VAL 628 (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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303A TYR* 4.5 7.4 - - + -
306A VAL* 3.9 22.0 - - + -
620A VAL* 3.4 17.8 - - + +
621A LEU* 3.4 57.2 - - + +
623A ARG 5.6 0.2 - - - +
626A GLY* 2.9 19.8 + - - +
627A ASN* 1.3 71.5 - - - +
629A TYR* 1.3 69.1 + - + +
631A ASN 3.2 2.4 + - - -
632A LEU* 2.6 36.3 + - + +
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Residues in contact with TYR 629 (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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2A ASN* 6.1 1.8 - - - -
303A TYR* 4.6 5.1 + + - -
306A VAL* 4.6 20.3 + - + -
307A ARG* 3.2 51.2 + - - -
308A ARG 4.6 2.3 + - - -
399A HIS* 4.7 4.9 - + - -
628A VAL* 1.3 88.3 - - + +
630A GLU* 1.3 67.0 + - + +
632A LEU* 3.3 3.0 + - + -
633A PHE 3.1 17.2 + - - -
141B MET* 3.5 42.3 - - + +
142B GLY* 4.8 3.1 + - - -
170B VAL* 3.7 19.8 - - + +
171B THR* 3.5 22.9 - - + -
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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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627A ASN* 4.6 15.6 + - + +
628A VAL 3.5 0.4 - - - -
629A TYR* 1.3 75.1 - - + +
631A ASN* 1.3 68.5 + - - +
633A PHE* 3.2 6.1 + - - +
634A GLU* 3.2 25.4 + - - +
170B VAL* 4.3 20.9 - - + -
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Residues in contact with ASN 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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620A VAL* 3.9 12.9 - - + +
623A ARG* 3.3 34.2 + - - +
627A ASN* 2.6 35.7 + - - +
628A VAL 3.2 3.0 + - - +
630A GLU* 1.3 78.4 + - - +
632A LEU* 1.3 65.0 - - - +
634A GLU* 3.3 10.8 + - - +
635A TRP* 3.0 25.1 + - - +
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Residues in contact with LEU 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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399A HIS* 4.0 35.9 - - + +
402A SER* 5.1 0.9 - - - +
404A SER* 3.3 35.9 - - - +
620A VAL* 3.5 11.8 - - + +
621A LEU* 4.5 10.3 - - + -
628A VAL* 2.6 26.1 + - + +
629A TYR* 3.3 7.1 + - + +
631A ASN* 1.3 73.6 - - - +
633A PHE* 1.3 60.5 + - - +
635A TRP* 3.5 7.3 - - + +
636A ALA* 3.2 21.8 + - - +
141B MET* 4.1 16.8 - - + -
175B TRP* 4.0 19.7 - - + +
226B ILE 5.8 0.2 - - - +
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Residues in contact with PHE 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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629A TYR 3.1 11.9 + - - +
630A GLU* 3.6 8.5 - - - +
631A ASN 3.1 0.6 - - - -
632A LEU* 1.3 75.1 - - - +
634A GLU* 1.3 77.9 + - - +
636A ALA* 3.3 2.6 + - - +
637A LYS* 3.0 57.6 + - - +
141B MET* 4.2 2.4 - - + +
170B VAL* 4.2 12.1 - - + -
173B ILE* 3.9 26.5 - - + -
175B TRP* 3.7 22.7 - + - -
222B THR* 4.9 7.2 - - + -
239B TYR* 3.8 37.9 - + - -
241B LYS* 5.4 6.5 - - + -
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Residues in contact with GLU 634 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630A GLU* 3.2 13.2 + - + +
631A ASN* 3.8 12.6 - - - +
633A PHE* 1.3 90.8 - - - +
635A TRP* 1.3 64.9 + - - +
637A LYS* 3.1 16.6 + - - +
638A LYS* 3.0 51.8 + - + +
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Residues in contact with TRP 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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50A ASP* 3.6 16.9 + - - -
52A ASN* 4.7 5.4 - - + -
53A PHE* 3.4 40.6 - + - -
402A SER* 3.7 12.1 - - - -
403A HIS* 4.0 11.2 + - + -
404A SER* 3.7 35.5 - - - +
620A VAL* 4.0 20.2 - - + +
631A ASN 3.0 17.5 + - - +
632A LEU* 3.5 9.6 - - + +
634A GLU* 1.3 78.2 - - - +
636A ALA* 1.3 76.3 + - + +
638A LYS* 3.2 12.9 + - - +
639A SER* 3.3 8.3 + - - -
226B ILE 3.4 22.7 - - - -
227B GLY* 3.9 6.7 - - - -
228B PRO* 3.4 27.8 - - + -
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Residues in contact with ALA 636 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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632A LEU 3.2 6.2 + - - +
633A PHE 3.8 2.0 - - - +
635A TRP* 1.3 84.8 - - + +
637A LYS* 1.3 60.6 + - - +
639A SER* 2.7 24.0 + - - -
642A ASN* 2.8 12.1 + - - -
175B TRP* 3.7 24.5 - - + -
225B ASP 3.9 1.6 - - - +
226B ILE* 3.3 38.6 - - - +
239B TYR* 4.6 4.5 - - + -
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Residues in contact with LYS 637 (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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633A PHE* 3.0 49.5 + - + +
634A GLU* 3.6 19.6 + - - +
636A ALA* 1.3 76.2 - - - +
638A LYS* 1.3 62.3 + - + +
639A SER 3.6 0.3 + - - +
642A ASN* 3.6 25.1 - - + +
222B THR* 5.2 10.0 - - - +
239B TYR* 4.4 16.3 - - - +
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Residues in contact with LYS 638 (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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49A GLU* 4.8 4.3 - - - +
53A PHE* 4.0 19.9 - - + -
634A GLU* 3.0 42.1 + - + +
635A TRP* 3.2 6.9 + - - +
636A ALA 3.1 0.2 - - - -
637A LYS* 1.3 78.3 - - + +
639A SER* 1.3 64.4 + - - +
640A PRO* 3.7 1.6 - - - +
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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