Contacts of the helix formed by residues 2121 - 2136 (chain A) in PDB entry 3CMT
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 THR2121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2119A PRO* 3.9 3.7 - - - +
2120A ASP* 1.3 85.0 - - + +
2122A GLY* 1.3 63.2 + - - +
2123A GLU* 3.7 15.1 + - - +
2124A GLN* 3.1 27.3 + - - +
2125A ALA* 3.1 20.8 + - - +
2150A THR 3.6 7.4 - - - -
2152A LYS* 3.8 36.0 - - + +
2155A ILE* 4.0 14.8 - - + -
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Residues in contact with GLY2122 (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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2121A THR* 1.3 68.7 - - - +
2123A GLU* 1.3 64.6 + - - +
2125A ALA* 3.2 6.9 + - - +
2126A LEU* 3.0 26.5 + - - +
2149A LEU* 3.9 30.5 - - - -
2150A THR 2.7 22.3 + - - +
2170A MET* 4.1 8.7 - - - -
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Residues in contact with GLU2123 (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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1159A ILE* 3.5 33.6 - - + +
1160A GLY* 3.9 14.4 - - - -
2121A THR* 3.8 4.8 - - - +
2122A GLY* 1.3 77.4 - - - +
2124A GLN* 1.3 52.2 + - - +
2126A LEU* 3.3 2.1 + - - +
2127A GLU* 2.8 40.1 + - + +
2151A PRO* 3.5 7.8 - - - +
2152A LYS* 2.7 47.1 + - + +
2166A LEU* 4.7 5.7 - - - +
2170A MET* 3.7 25.3 - - + +
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Residues in contact with GLN2124 (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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2118A GLN 4.9 0.3 - - - +
2119A PRO* 3.4 9.3 - - + +
2120A ASP* 3.4 49.0 + - - +
2121A THR* 3.1 20.9 + - - +
2123A GLU* 1.3 79.9 - - - +
2125A ALA* 1.3 56.3 + - - +
2127A GLU* 3.2 1.7 + - - +
2128A ILE* 2.9 43.9 + - + +
3021A PHE* 3.4 54.9 + - + +
3025A SER* 4.3 11.4 - - - -
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Residues in contact with ALA2125 (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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2093A ILE* 4.0 13.4 - - + +
2119A PRO* 3.6 29.3 - - + +
2121A THR 3.1 6.4 + - - +
2122A GLY 3.3 8.7 - - - +
2124A GLN* 1.3 80.1 - - - +
2126A LEU* 1.3 57.7 + - + +
2128A ILE* 3.5 6.5 + - - +
2129A CYS* 3.2 29.7 + - - -
2143A VAL* 5.5 1.8 - - + -
2149A LEU* 3.8 23.8 - - + -
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Residues in contact with LEU2126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1159A ILE* 3.5 27.6 - - + +
2122A GLY 3.0 20.4 + - - +
2123A GLU 3.9 2.2 - - - +
2125A ALA* 1.3 73.9 - - + +
2127A GLU* 1.3 61.9 + - - +
2128A ILE 3.2 0.4 - - - -
2129A CYS* 3.3 11.4 + - - +
2130A ASP 3.0 23.2 + - - -
2143A VAL* 5.6 1.6 - - + -
2149A LEU* 4.1 7.2 - - + -
2170A MET* 3.9 22.7 - - + -
2171A MET* 3.5 36.6 - - + -
2174A ALA* 3.8 21.8 - - + -
2178A LEU* 4.5 5.8 - - + +
2191A PHE* 4.1 23.6 - - + -
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Residues in contact with GLU2127 (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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1158A GLU* 3.3 32.5 - - - +
1159A ILE* 3.0 39.7 + - + +
2123A GLU 2.8 20.0 + - - +
2124A GLN 3.6 3.8 - - - +
2126A LEU* 1.3 72.9 - - - +
2128A ILE* 1.3 59.4 + - - +
2130A ASP* 3.4 7.9 + - - +
2131A ALA* 3.0 27.4 + - - +
2134A ARG* 5.1 8.1 + - - -
2177A LYS* 3.5 16.5 + - - -
3020A GLN* 4.5 5.2 - - - +
3021A PHE* 3.7 20.4 - - + -
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Residues in contact with ILE2128 (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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2093A ILE* 3.9 22.2 - - + -
2117A SER* 3.5 22.9 - - - +
2119A PRO* 4.7 1.1 - - + -
2124A GLN* 2.9 41.1 + - + +
2125A ALA* 3.6 8.5 - - - +
2126A LEU 3.2 0.2 - - - -
2127A GLU* 1.3 74.2 - - - +
2129A CYS* 1.3 64.7 + - - +
2131A ALA* 3.2 7.4 + - - +
2132A LEU* 3.0 34.5 + - + +
3017A ILE* 3.8 34.5 - - + -
3021A PHE* 4.3 8.7 - - + -
3025A SER* 4.6 3.6 - - - +
3026A ILE* 4.3 8.5 - - + -
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Residues in contact with CYS2129 (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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2093A ILE* 4.1 6.1 - - - -
2125A ALA 3.2 19.0 + - - -
2126A LEU* 3.4 15.5 - - - +
2128A ILE* 1.3 77.0 - - - +
2130A ASP* 1.3 51.8 + - - +
2132A LEU* 3.3 3.6 + - - +
2133A ALA* 2.7 36.6 + - - +
2141A ILE* 3.9 27.6 - - + +
2143A VAL* 3.7 30.1 - - - -
2178A LEU* 4.1 17.0 - - + -
2189A LEU* 4.8 8.7 - - + -
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Residues in contact with ASP2130 (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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1155A ILE 5.1 0.3 - - - +
1159A ILE* 4.5 2.7 - - + -
2126A LEU 3.0 16.8 + - - +
2127A GLU* 3.7 12.8 - - - +
2129A CYS* 1.3 76.0 - - - +
2131A ALA* 1.3 58.0 + - - +
2133A ALA* 3.3 1.9 + - - +
2134A ARG* 2.5 60.3 + - - +
2177A LYS* 3.4 36.5 + - - +
2178A LEU* 3.6 20.5 - - + +
2181A ASN* 2.8 23.3 - - - +
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Residues in contact with ALA2131 (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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2127A GLU 3.0 13.5 + - - +
2128A ILE 3.5 7.9 - - - +
2130A ASP* 1.3 76.9 - - - +
2132A LEU* 1.3 58.3 + - - +
2134A ARG* 3.6 22.0 - - - +
2135A SER* 3.0 28.1 + - - -
3013A ALA* 4.3 8.9 - - + +
3016A GLN* 5.2 9.6 - - + +
3017A ILE* 4.0 25.1 - - + -
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Residues in contact with LEU2132 (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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2091A ALA* 3.7 29.6 - - + -
2093A ILE* 4.7 4.7 - - + -
2115A LEU* 4.7 2.5 - - + -
2128A ILE* 3.0 37.1 + - + +
2129A CYS 3.7 2.9 - - - +
2131A ALA* 1.3 72.2 - - - +
2133A ALA* 1.3 67.5 - - - +
2135A SER* 2.7 24.9 + - - +
2136A GLY* 3.6 2.1 + - - -
2138A VAL* 3.8 29.0 + - + +
2141A ILE* 3.8 17.3 - - + -
3010A LEU* 5.3 0.9 - - + -
3013A ALA* 4.9 4.0 - - + -
3014A LEU* 4.5 17.3 - - + -
3017A ILE* 4.1 17.0 - - + -
3026A ILE* 4.3 10.1 - - + -
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Residues in contact with ALA2133 (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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2129A CYS 2.7 22.4 + - - +
2130A ASP* 3.5 7.4 - - - +
2132A LEU* 1.3 74.6 - - - +
2134A ARG* 1.3 57.6 + - - +
2136A GLY 3.2 2.1 + - - -
2141A ILE* 4.2 4.1 - - - +
2178A LEU* 4.8 2.2 - - + -
2181A ASN* 4.0 21.3 - - + +
2182A LEU* 4.0 25.8 - - + -
2185A SER* 2.5 31.3 + - - -
2187A THR* 4.1 9.4 + - - -
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Residues in contact with ARG2134 (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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1155A ILE 5.6 2.2 + - - -
2127A GLU* 5.1 8.3 + - - -
2130A ASP* 2.5 54.6 + - - +
2131A ALA* 3.6 24.3 - - - +
2133A ALA* 1.3 73.2 - - - +
2135A SER* 1.3 64.4 + - - +
2136A GLY* 3.2 1.6 + - - -
2177A LYS* 5.1 1.6 - - - +
2181A ASN* 3.2 34.2 + - - +
2185A SER* 4.2 4.8 + - - -
3016A GLN* 5.2 9.7 - - - +
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Residues in contact with SER2135 (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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2131A ALA 3.0 15.7 + - - -
2132A LEU* 2.7 22.3 + - - +
2134A ARG* 1.3 76.7 - - - +
2136A GLY* 1.3 59.7 + - - +
2137A ALA* 3.1 18.8 + - - +
2138A VAL* 4.1 3.3 + - - +
3006A LYS* 6.0 0.2 - - - -
3009A ALA* 3.6 31.6 - - - +
3010A LEU* 5.0 0.7 - - - +
3013A ALA* 3.8 22.8 - - - +
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Residues in contact with GLY2136 (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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2132A LEU 3.6 0.6 + - - -
2133A ALA 3.2 11.8 + - - -
2134A ARG 3.1 4.8 - - - -
2135A SER* 1.3 78.4 + - - +
2137A ALA* 1.3 58.5 + - - +
2138A VAL 3.6 5.1 - - - +
2139A ASP* 5.7 0.3 - - - +
2185A SER* 4.0 23.2 - - - +
3006A LYS* 3.8 17.1 - - - +
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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