Contacts of the helix formed by residues 110 - 118 (chain A) in PDB entry 5Z7R
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 GLY 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A GLY* 4.9 2.2 - - - -
109A LEU* 1.3 70.0 - - - +
111A GLY* 1.3 64.9 + - - -
112A GLY 2.9 1.2 + - - -
113A CYS* 3.0 4.5 + - - +
114A GLU* 3.0 26.7 + - - +
131A GLY 2.9 12.3 + - - -
132A GLN* 3.5 6.5 - - - +
133A PRO* 3.4 13.2 - - - +
134A GLU* 3.0 20.4 - - - -
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Residues in contact with GLY 111 (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 LEU* 3.5 21.7 - - - +
65A GLY* 4.4 9.8 - - - -
66A ALA* 4.9 2.5 - - - +
90A PHE* 3.6 3.1 - - - -
109A LEU 3.1 2.2 + - - -
110A GLY* 1.3 69.7 - - - -
112A GLY* 1.3 54.9 + - - +
114A GLU* 3.0 18.7 + - - -
115A ILE* 2.9 22.7 + - - +
134A GLU* 3.8 1.6 + - - -
143A PHE* 4.0 17.5 - - - -
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 3.4 9.9 - - - -
63A VAL* 3.6 35.5 - - - +
65A GLY 4.4 0.8 - - - +
108A ALA* 4.1 7.1 - - - +
109A LEU 2.7 18.6 + - - -
111A GLY* 1.3 70.5 - - - -
113A CYS* 1.3 62.1 + - - +
114A GLU 3.2 0.2 - - - -
115A ILE* 3.2 6.6 - - - +
116A ALA* 3.2 17.7 + - - +
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Residues in contact with CYS 113 (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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108A ALA* 3.5 19.7 - - - +
110A GLY 3.0 8.7 + - - +
112A GLY* 1.3 73.5 - - - +
114A GLU* 1.3 58.6 + - - +
116A ALA* 3.1 6.7 + - - +
117A MET* 2.9 48.4 + - - +
130A PHE* 4.2 22.0 - - - -
131A GLY 3.4 22.0 - - - +
132A GLN* 3.4 20.4 - - - +
149A LEU* 5.0 4.3 - - - -
178A LEU* 4.6 6.3 - - - -
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Residues in contact with GLU 114 (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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90A PHE* 3.7 5.4 - - + -
110A GLY 3.0 11.9 + - - +
111A GLY* 3.0 29.6 + - - +
112A GLY 3.2 0.2 - - - -
113A CYS* 1.3 78.4 - - - +
115A ILE* 1.3 60.8 + - - +
117A MET* 3.4 9.6 + - + +
118A SER* 2.7 26.9 + - - -
132A GLN* 3.7 12.6 - - - +
134A GLU* 3.6 5.1 - - - +
141A PRO* 3.4 2.1 - - - +
142A GLY 3.4 9.1 + - - -
143A PHE* 2.9 42.7 + - - +
144A GLY 4.4 0.7 - - - -
145A GLY* 2.8 40.4 + - - +
148A ARG* 4.8 1.7 - - - +
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Residues in contact with ILE 115 (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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19A ILE* 4.5 13.2 - - + -
28A LEU* 4.9 6.5 - - + -
33A LEU* 5.9 0.2 - - + -
36A MET* 4.5 20.4 - - + -
54A LEU* 3.9 18.6 - - + -
62A PHE* 3.5 19.5 - - + -
63A VAL* 4.4 9.2 - - + -
90A PHE* 3.4 41.2 - - + -
93A LEU* 4.1 12.5 - - + +
111A GLY 2.9 11.8 + - - +
112A GLY* 3.2 16.2 - - - +
114A GLU* 1.3 76.8 - - - +
116A ALA* 1.3 66.9 + - - +
118A SER* 3.0 15.9 + - - -
119A CYS* 3.5 8.9 + - - -
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Residues in contact with ALA 116 (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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62A PHE* 3.8 14.4 - - + -
102A ALA* 4.2 11.4 - - + -
104A VAL* 4.2 18.8 - - + -
108A ALA* 5.3 0.4 - - + -
112A GLY 3.2 9.8 + - - +
113A CYS* 3.1 11.1 + - - +
115A ILE* 1.3 83.7 - - - +
117A MET* 1.3 56.8 + - + +
118A SER 3.0 0.2 - - - -
119A CYS* 3.1 19.5 + - - +
122A ARG* 3.2 26.3 + - + +
130A PHE* 4.9 6.3 - - + -
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Residues in contact with MET 117 (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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94A GLU* 4.3 3.1 - - - +
113A CYS* 2.9 25.7 + - - +
114A GLU* 3.7 12.1 - - - +
115A ILE 3.2 0.2 - - - -
116A ALA* 1.3 74.3 - - + +
118A SER* 1.3 59.3 + - - +
119A CYS 3.3 6.5 + - - +
122A ARG* 3.9 11.8 + - - +
132A GLN* 3.4 29.6 - - - +
145A GLY* 4.1 10.1 - - - -
148A ARG* 3.5 21.8 + - + -
149A LEU* 3.6 52.5 - - + +
152A LEU* 3.8 20.6 - - + +
178A LEU* 4.1 16.2 - - + -
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Residues in contact with SER 118 (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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90A PHE* 3.5 31.7 - - - +
93A LEU* 3.9 8.4 - - - +
94A GLU* 3.2 31.2 + - - +
114A GLU 2.7 19.6 + - - -
115A ILE* 3.0 12.6 + - - -
117A MET* 1.3 77.8 - - - +
119A CYS* 1.3 59.8 + - - +
148A ARG* 3.4 28.9 + - - +
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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