Contacts of the helix formed by residues 118 - 127 (chain A) in PDB entry 1R6Q
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 SER 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.4 8.4 - - - +
28A GLU* 3.7 10.5 - - - -
83A SER* 4.4 8.7 - - - -
112A ILE 4.2 1.6 + - - -
115A GLU* 2.8 33.5 + - - +
116A GLN 4.5 1.7 - - - +
117A GLU* 1.3 80.8 - - - +
119A GLN* 1.3 63.2 + - - +
120A ALA* 3.7 2.9 + - - +
121A ALA* 3.1 18.5 + - - +
122A TYR* 3.2 14.7 + - - +
25C PRO* 3.7 7.5 - - - +
79C GLU* 4.6 9.6 - - - -
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Residues in contact with GLN 119 (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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28A GLU* 3.1 8.6 + - + +
61A PHE* 3.5 61.3 - - + +
117A GLU 4.1 0.4 + - - -
118A SER* 1.3 69.8 - - - +
120A ALA* 1.3 60.5 + - - +
122A TYR* 3.2 28.7 + - - +
123A LEU* 2.8 46.3 + - + +
24C PRO* 4.4 6.3 - - - +
25C PRO* 3.3 24.9 - - + +
79C GLU* 5.0 0.4 + - - +
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Residues in contact with ALA 120 (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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27A VAL* 3.8 30.3 - - + +
28A GLU* 2.8 23.7 + - + +
31A LEU* 3.8 22.5 - - + +
58A LEU* 4.7 2.2 - - - -
112A ILE* 3.9 7.2 - - + -
118A SER* 4.1 0.2 - - - +
119A GLN* 1.3 76.3 - - - +
121A ALA* 1.3 56.8 + - - +
123A LEU* 3.3 5.6 + - - +
124A LEU* 3.0 32.2 + - - +
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Residues in contact with ALA 121 (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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112A ILE* 3.7 19.4 - - - +
113A PHE* 4.3 5.8 - - - +
115A GLU 3.4 14.4 - - - +
116A GLN* 4.9 1.6 - - - -
118A SER* 3.1 18.6 + - - +
120A ALA* 1.3 75.6 - - - +
122A TYR* 1.3 66.8 + - - +
124A LEU* 3.4 7.1 + - - +
125A ARG* 3.1 50.4 + - - +
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Residues in contact with TYR 122 (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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116A GLN 5.7 0.9 + - - +
118A SER 3.2 11.3 + - - +
119A GLN* 3.2 36.0 + - - +
121A ALA* 1.3 79.5 - - - +
123A LEU* 1.3 71.7 + - + +
125A ARG* 3.3 9.8 + - - +
126A LYS* 2.9 48.4 + - + +
22C LEU* 4.2 27.9 + - + +
23C LYS 3.7 18.4 - - - +
24C PRO* 3.6 37.3 - - + +
25C PRO* 3.9 11.4 - - + -
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Residues in contact with LEU 123 (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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54A LEU* 3.9 13.5 - - + -
57A GLU* 4.0 41.5 - - + +
58A LEU* 3.8 31.9 - - + -
61A PHE* 5.5 0.7 - - + -
119A GLN* 2.8 36.0 + - + +
120A ALA* 3.8 4.5 - - - +
122A TYR* 1.3 94.7 - - + +
124A LEU* 1.3 63.8 + - - +
126A LYS* 3.2 11.2 + - + +
127A HIS* 3.0 31.7 + - - -
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Residues in contact with LEU 124 (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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31A LEU* 3.9 19.1 - - + -
44A LEU* 3.9 28.5 - - + -
49A VAL* 6.0 0.2 - - + -
54A LEU* 4.5 9.0 - - + -
109A LEU* 3.8 25.4 - - + -
112A ILE* 3.9 22.0 - - + -
113A PHE* 3.8 29.4 - - + -
120A ALA 3.0 20.6 + - - +
121A ALA* 3.8 6.1 - - - +
122A TYR 3.3 0.2 - - - -
123A LEU* 1.3 75.0 - - - +
125A ARG* 1.3 60.9 + - - +
127A HIS* 3.2 11.2 + - + -
128A GLU 3.4 0.2 + - - -
129A VAL* 3.0 32.5 + - + +
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Residues in contact with ARG 125 (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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113A PHE* 2.5 50.8 + - + +
116A GLN* 3.9 30.2 + - - +
121A ALA* 3.1 30.1 + - - +
122A TYR* 3.8 5.8 - - - +
124A LEU* 1.3 73.0 - - - +
126A LYS* 1.3 61.1 + - - +
128A GLU* 3.1 18.8 + - - +
129A VAL 3.6 16.4 - - - +
130A SER* 5.4 1.8 - - - +
22C LEU* 3.5 37.3 - - + +
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Residues in contact with LYS 126 (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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57A GLU* 3.3 25.6 + - - +
122A TYR* 2.9 39.0 + - + +
123A LEU* 3.2 22.9 + - + +
125A ARG* 1.3 76.1 - - - +
127A HIS* 1.3 63.3 + - + +
128A GLU* 3.1 11.7 + - - +
22C LEU* 4.0 8.9 - - + +
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Residues in contact with HIS 127 (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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47A CYS 4.8 3.8 - - - +
48A SER 5.6 0.3 - - - +
49A VAL* 4.1 30.7 - - + +
50A ASP* 4.0 28.1 + - + +
53A ALA* 4.3 9.0 - - + -
54A LEU* 3.9 21.3 - - + +
57A GLU* 2.7 33.1 + - - -
123A LEU* 3.0 27.5 + - - +
124A LEU* 3.2 6.4 + - + +
126A LYS* 1.3 81.9 - - + +
128A GLU* 1.3 69.5 + - - +
129A VAL* 3.3 9.7 + - + +
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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