Contacts of the helix formed by residues 2124 - 2128 (chain A) in PDB entry 4YNM
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 CYS2124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2093A CYS* 3.7 23.1 - - - -
2094A LYS 3.8 23.3 - - - -
2095A LYS* 3.3 23.1 - - - -
2103A GLY* 3.9 5.2 - - - -
2104A CYS* 3.5 27.1 - - - -
2122A CYS* 3.1 9.4 - - - -
2123A PRO* 1.3 77.4 - - - +
2125A GLY* 1.3 64.5 + - - +
2126A GLU 3.1 0.9 + - - -
2127A GLN* 3.0 19.7 + - + +
2128A CYS* 3.9 16.4 - - - +
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Residues in contact with GLY2125 (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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2095A LYS* 3.5 12.8 - - - -
2119A PRO* 5.8 5.2 - - - +
2122A CYS* 3.1 17.9 + - - +
2123A PRO 3.2 2.4 + - - -
2124A CYS* 1.3 74.2 - - - +
2126A GLU* 1.3 68.5 + - - +
2128A CYS* 3.3 18.5 + - - +
2131A GLN* 4.4 5.0 + - - -
2135A ARG* 4.7 2.9 + - - -
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Residues in contact with GLU2126 (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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2095A LYS* 4.2 6.6 - - - +
2102A LYS* 4.3 9.4 + - - -
2119A PRO* 5.7 2.8 - - - +
2124A CYS 3.1 1.2 + - - -
2125A GLY* 1.3 72.8 - - - +
2127A GLN* 1.3 59.7 + - - +
2128A CYS 3.2 10.4 + - - +
2135A ARG* 3.3 31.0 + - - +
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Residues in contact with GLN2127 (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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2095A LYS* 4.1 12.1 - - - +
2096A PRO* 3.2 30.5 + - + +
2098A ASP 3.3 4.7 + - - -
2099A ASP* 2.6 42.4 + - - +
2101A ARG 3.2 26.5 - - - +
2102A LYS* 3.7 21.6 - - + +
2103A GLY* 2.9 29.2 + - - +
2124A CYS* 3.0 11.3 + - - +
2126A GLU* 1.3 76.6 - - + +
2128A CYS* 1.3 65.1 + - - +
2129A CYS 3.0 2.3 + - - -
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Residues in contact with CYS2128 (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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2102A LYS* 4.7 2.9 + - - -
2103A GLY 4.0 3.6 - - - -
2104A CYS* 3.7 2.0 - - - -
2117A CYS* 3.4 7.4 - - - -
2122A CYS* 3.3 8.5 - - - -
2124A CYS* 3.5 8.7 + - + -
2125A GLY 3.3 12.1 + - - +
2126A GLU 3.2 5.1 - - - +
2127A GLN* 1.3 75.3 - - - +
2129A CYS* 1.3 59.4 + - - +
2130A ASN* 3.3 15.1 + - - -
2131A GLN* 3.2 28.8 + - - +
2135A ARG* 3.6 17.2 + - - -
2302A ZN 2.0 39.7 - - - -
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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