Contacts of the helix formed by residues 113 - 122 (chain B) in PDB entry 5M4G
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 113 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 6.1 0.2 - - - -
110B LYS* 6.1 0.8 - - - +
111B ILE 3.6 2.8 + - - -
112B HIS* 1.3 78.9 - - - +
114B LYS* 1.3 63.8 - - - +
115B GLU* 3.4 10.4 + - - +
116B HIS* 2.9 37.5 + - - +
117B PHE* 3.3 10.8 - - - -
128B TYR* 5.3 3.4 - - - -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.6 2.5 - - + -
113B SER* 1.3 74.1 - - - +
115B GLU* 1.3 65.9 + - + +
117B PHE* 3.1 4.9 + - - -
118B LYS* 3.0 19.3 + - - +
126B VAL* 3.6 46.7 + - + +
127B GLN* 3.9 21.8 + - - +
128B TYR* 3.5 55.1 + - + -
131B GLU* 4.8 4.9 + - - -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B SER* 3.2 9.6 + - - +
114B LYS* 1.3 76.6 - - + +
116B HIS* 1.3 66.6 + - - +
118B LYS* 3.2 30.2 + - - +
119B GLU* 3.0 25.1 + - - +
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Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B HIS* 3.4 48.4 + + + -
113B SER* 2.9 28.7 + - - +
115B GLU* 1.3 76.7 - - - +
117B PHE* 1.3 71.2 + + - +
119B GLU* 3.4 8.0 + - - +
120B LYS* 2.9 49.0 + - + +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLU* 3.5 32.8 - - + -
95B LEU* 4.4 4.3 - - + -
97B VAL* 4.0 37.9 - - + -
98B PRO* 5.9 0.7 - - + -
112B HIS* 3.7 40.2 - + + -
113B SER 3.3 17.9 + - - -
114B LYS* 3.1 7.2 + - - +
116B HIS* 1.3 86.8 - + - +
118B LYS* 1.3 66.4 + - - +
120B LYS* 4.1 3.1 - - + -
121B TYR* 3.0 46.9 + + - +
126B VAL* 4.0 14.9 - - + +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LYS 3.0 9.6 + - - +
115B GLU* 3.2 35.2 + - - +
117B PHE* 1.3 77.2 - - - +
119B GLU* 1.3 55.8 + - - +
122B ALA* 2.9 29.6 + - - -
123B VAL* 3.4 20.7 + - + +
124B ASP* 3.2 28.1 + - - +
125B ASP* 4.5 7.3 + - - +
126B VAL* 3.5 21.7 - - + +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO* 3.5 21.7 - - + +
115B GLU* 3.0 16.6 + - - +
116B HIS* 3.7 6.9 + - - +
118B LYS* 1.3 78.4 - - - +
120B LYS* 1.3 62.2 + - - +
121B TYR 3.4 0.2 + - - -
122B ALA* 3.7 3.0 + - - +
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLY 5.5 2.8 + - - -
7B PRO* 3.8 9.0 - - - +
20B LEU* 3.4 22.5 - - - +
78B THR* 4.0 6.6 + - - -
79B GLU* 2.8 25.9 + - - +
112B HIS* 6.4 0.4 - - - -
116B HIS* 2.9 40.1 + - + +
117B PHE* 3.3 7.8 + - + +
119B GLU* 1.3 79.3 - - - +
121B TYR* 1.3 92.4 + - + +
504B GOL 3.6 32.0 + - - +
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Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 3.8 32.0 - - + +
23B PHE* 6.1 0.3 - - - +
27B ARG* 4.4 6.9 + - - -
75B PHE 3.9 12.3 - - - +
76B GLY 3.4 20.0 - - - -
77B VAL* 3.6 15.0 - - + -
78B THR* 3.1 19.8 + - - +
79B GLU* 2.6 31.7 + - - -
95B LEU* 3.7 16.8 - - + -
117B PHE* 3.0 33.2 + + - +
120B LYS* 1.3 106.1 - - + +
122B ALA* 1.3 72.9 + - - +
123B VAL* 3.3 21.2 + - + +
282B TYR* 4.6 1.8 - - - -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO* 4.2 23.3 - - + -
20B LEU* 4.5 8.5 - - + -
21B ALA* 5.8 0.9 - - - +
24B ALA* 5.2 2.9 - - - +
27B ARG* 3.5 12.6 + - - -
118B LYS 2.9 12.9 + - - -
119B GLU 3.7 2.6 + - - +
120B LYS 3.6 1.6 - - - -
121B TYR* 1.3 80.5 - - - +
123B VAL* 1.3 60.6 + - - +
124B ASP* 5.8 0.2 - - - -
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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