Contacts of the helix formed by residues 127 - 136 (chain A) in PDB entry 2QMQ
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 MET 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 3.6 24.5 - - + +
47A TYR* 3.6 40.2 - - + +
48A GLY 4.4 3.4 - - - +
50A VAL* 3.7 35.0 - - + -
68A TYR* 5.6 0.4 - - - -
103A PRO* 3.9 11.0 - - + -
119A PRO* 3.8 16.8 - - + -
123A GLN 3.6 8.5 - - - +
124A LEU* 3.5 22.4 - - + +
125A ALA 3.1 0.8 - - - -
126A ASP* 1.3 78.4 - - - +
128A ILE* 1.3 66.3 + - + +
129A PRO 3.3 1.1 - - - -
130A CYS* 3.0 24.0 + - - +
131A ILE* 3.3 14.7 + - + +
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Residues in contact with ILE 128 (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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66A PHE* 3.8 30.7 - - + -
68A TYR* 4.3 8.3 - - + -
124A LEU 4.0 6.5 - - - +
125A ALA 3.5 11.7 - - - +
127A MET* 1.3 78.3 - - + +
129A PRO* 1.3 65.3 - - + +
131A ILE* 3.1 12.5 + - + +
132A LEU* 3.0 31.5 + - + +
140A ILE* 5.3 0.2 - - + -
151A ILE* 4.0 19.7 - - + -
152A LEU* 3.7 29.4 - - + -
155A TYR* 3.6 36.3 - - + -
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Residues in contact with PRO 129 (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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4A 2PE 3.8 31.2 - - - +
125A ALA 3.5 10.1 - - - +
126A ASP* 3.4 19.3 - - - +
128A ILE* 1.3 88.8 - - + +
130A CYS* 1.4 57.5 + - - +
132A LEU* 4.0 0.3 - - - +
133A GLN* 2.8 44.2 + - - +
155A TYR* 3.9 10.3 - - + -
159A HIS* 3.7 25.8 - - + +
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Residues in contact with CYS 130 (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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43A VAL* 4.0 21.2 - - + +
44A GLU 4.8 3.4 - - - +
45A THR* 4.0 23.3 - - + -
46A PRO* 4.9 6.1 - - - -
126A ASP 4.3 11.9 - - - -
127A MET 3.0 12.9 + - - +
129A PRO* 1.4 75.3 - - - +
131A ILE* 1.3 58.7 + - - +
133A GLN* 3.9 11.8 - - - +
134A TYR* 3.0 29.8 + - - +
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Residues in contact with ILE 131 (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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43A VAL* 3.9 19.3 - - + -
50A VAL* 3.9 21.1 - - + -
52A PHE* 3.8 39.0 - - + -
66A PHE* 3.9 25.1 - - + -
68A TYR* 5.9 0.2 - - + -
98A VAL* 4.3 0.7 - - + -
100A VAL* 4.0 24.5 - - + -
127A MET* 3.7 13.2 - - + +
128A ILE* 3.1 14.0 + - + +
130A CYS* 1.3 74.8 - - - +
132A LEU* 1.3 62.5 + - - +
134A TYR* 3.3 4.5 + - - +
135A LEU* 3.1 29.3 + - + +
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Residues in contact with LEU 132 (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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4A 2PE 3.7 17.1 - - - +
66A PHE* 3.8 18.4 - - + -
128A ILE* 3.0 25.3 + - + +
131A ILE* 1.3 75.5 - - + +
133A GLN* 1.3 55.3 + - - +
135A LEU* 3.4 4.0 + - + +
136A ASN* 2.8 30.0 + - - -
137A PHE* 3.0 45.1 + - + +
138A SER 5.8 0.2 - - - -
140A ILE* 3.7 30.5 - - + -
155A TYR* 3.3 33.7 - - + +
162A THR* 5.0 4.3 - - - +
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Residues in contact with GLN 133 (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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4A 2PE 3.0 89.2 + - - +
129A PRO* 2.8 29.5 + - - +
130A CYS* 3.9 11.2 - - - +
132A LEU* 1.3 75.4 - - - +
134A TYR* 1.3 65.2 + - - +
136A ASN* 3.3 12.0 + - - +
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Residues in contact with TYR 134 (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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41A HIS* 2.6 49.6 + + + +
42A SER 4.3 11.1 + - - -
43A VAL* 3.6 20.0 - - + -
52A PHE* 3.7 16.6 - + - -
130A CYS 3.0 19.0 + - - +
131A ILE 3.3 4.2 + - - +
133A GLN* 1.3 76.4 - - - +
135A LEU* 1.3 69.7 + - + +
136A ASN* 5.0 0.5 - - - +
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Residues in contact with LEU 135 (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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0A HIS* 6.0 1.3 - - + -
41A HIS* 5.1 5.2 - - + +
52A PHE* 3.9 22.9 - - + -
54A VAL* 4.2 15.3 - - + -
98A VAL* 3.8 35.2 - - + -
131A ILE* 3.1 21.7 + - + +
132A LEU* 4.0 5.6 - - + +
134A TYR* 1.3 91.7 - - + +
136A ASN* 1.3 69.4 + - - +
137A PHE* 3.3 40.2 - - + -
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Residues in contact with ASN 136 (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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4A 2PE 3.5 26.5 - - - +
132A LEU 2.8 10.2 + - - -
133A GLN 3.3 12.0 + - - +
134A TYR 3.3 1.3 - - - +
135A LEU* 1.3 80.8 - - - +
137A PHE* 1.3 61.3 - - - +
138A SER* 4.0 3.5 + - - -
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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