Contacts of the helix formed by residues 115 - 127 (chain B) in PDB entry 4QKH
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B GLN* 4.9 2.3 + - - -
113B VAL* 3.6 4.9 - - - +
114B GLU* 1.3 78.6 - - - +
116B PHE* 1.3 63.6 + - - +
117B GLN* 3.5 15.2 + - - +
118B GLU* 3.1 31.6 + - - +
119B LEU* 3.1 21.1 + - - +
154B GLN* 3.2 19.4 - - - +
155B PHE* 4.5 1.9 - - - -
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Residues in contact with PHE 116 (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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115B SER* 1.3 71.2 - - - +
117B GLN* 1.3 66.8 + - + +
119B LEU* 3.2 27.3 + - + +
120B ASN* 3.0 54.5 + - - -
154B GLN* 3.4 26.6 + - - +
155B PHE* 4.6 5.4 - - + -
156B PRO* 6.1 2.0 - - + -
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Residues in contact with GLN 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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77A GLU* 3.3 22.3 + - - +
82B PHE* 3.8 16.4 - - + -
83B GLN* 3.4 20.0 + - - +
115B SER* 3.3 11.5 + - - +
116B PHE* 1.3 78.9 - - - +
118B GLU* 1.3 63.3 + - - +
120B ASN* 3.4 8.8 + - - +
121B PHE* 3.1 23.2 + - - +
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Residues in contact with GLU 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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82B PHE* 4.0 25.6 - - + -
83B GLN* 4.4 8.3 - - - +
85B LYS* 2.9 39.1 + - - +
87B PHE* 4.7 10.2 - - + -
112B GLN 3.5 3.1 - - - +
113B VAL* 3.6 8.1 - - + -
114B GLU* 2.7 35.6 + - - +
115B SER* 3.1 22.8 + - - +
117B GLN* 1.3 74.6 - - - +
119B LEU* 1.3 67.3 + - - +
121B PHE* 3.2 4.3 + - - +
122B LEU* 3.0 29.5 + - + +
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Residues in contact with LEU 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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113B VAL* 3.8 12.9 - - + +
115B SER 3.1 13.5 + - - +
116B PHE* 3.5 26.0 - - + +
118B GLU* 1.3 77.9 - - - +
120B ASN* 1.3 58.1 + - - +
122B LEU* 3.3 3.2 + - - +
123B LEU* 3.0 49.2 + - + +
155B PHE* 3.7 40.8 - - + -
166B LEU* 3.6 35.2 - - + -
170B GLY* 4.9 8.7 - - - -
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Residues in contact with ASN 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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116B PHE* 3.0 59.7 + - - +
117B GLN* 3.9 7.1 - - - +
118B GLU 3.2 0.2 - - - -
119B LEU* 1.3 74.7 - - - +
121B PHE* 1.3 60.7 + - - +
123B LEU* 3.9 14.8 - - - +
124B ARG* 3.1 29.5 + - - +
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Residues in contact with PHE 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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80A ILE* 4.1 10.8 - - + -
125A TYR* 3.8 36.3 - + - +
80B ILE* 3.5 34.3 - - + -
82B PHE* 3.7 43.5 - + + -
87B PHE* 3.6 28.7 - + + -
89B PHE* 4.7 7.4 - + - -
117B GLN 3.1 13.7 + - - +
118B GLU 3.4 9.0 - - - +
120B ASN* 1.3 74.9 - - - +
122B LEU* 1.3 84.2 + - + +
124B ARG* 3.3 4.2 + - - +
125B TYR* 3.3 20.5 + - + +
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Residues in contact with LEU 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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87B PHE* 3.8 24.9 - - + -
89B PHE* 3.5 29.0 - - + -
111B ALA* 4.7 3.8 - - + -
113B VAL* 3.6 33.7 - - + -
118B GLU* 3.0 19.4 + - + +
119B LEU* 3.7 5.4 - - - +
121B PHE* 1.3 92.8 - - + +
123B LEU* 1.3 57.9 + - - +
125B TYR* 3.4 0.7 + - - -
126B LYS* 3.0 33.9 + - - +
166B LEU* 3.8 23.1 - - + -
183B ILE* 4.2 11.0 - - + -
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Residues in contact with LEU 123 (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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119B LEU* 3.0 42.1 + - + +
120B ASN* 4.0 14.8 - - - +
122B LEU* 1.3 76.4 - - - +
124B ARG* 1.4 61.7 + - - +
126B LYS* 3.8 24.3 + - - +
127B GLY 4.6 1.7 + - - -
166B LEU* 4.2 14.4 - - + -
167B ASN 3.2 27.4 - - - +
168B ASP 4.6 9.4 - - - +
169B LYS 4.5 4.3 - - - +
170B GLY* 4.1 19.1 - - - +
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Residues in contact with ARG 124 (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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89A PHE* 3.7 27.3 + - - +
90A SER 5.4 2.4 + - - -
91A ASP* 5.0 9.3 + - - -
124A ARG 3.8 11.3 - - - +
125A TYR* 2.9 55.3 + - + +
126A LYS* 3.0 27.4 + - - +
127A GLY* 5.4 2.4 - - - +
131A HIS* 4.8 2.4 + - - -
120B ASN 3.1 18.1 + - - +
121B PHE 3.7 4.7 - - - +
122B LEU 3.3 0.2 - - - -
123B LEU* 1.4 78.2 - - - +
125B TYR* 1.3 59.5 + - - +
127B GLY* 4.6 2.4 + - - -
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Residues in contact with TYR 125 (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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82A PHE* 5.5 0.9 - - - -
121A PHE* 3.5 41.3 - + - +
124A ARG* 2.8 84.8 + - + +
125A TYR* 3.9 27.1 - + + -
80B ILE* 4.1 14.4 - - + +
89B PHE* 3.6 44.0 - + + -
121B PHE* 3.3 17.5 + + + +
122B LEU 4.1 2.0 - - - +
124B ARG* 1.3 79.2 - - - +
126B LYS* 1.3 62.1 + - - +
127B GLY 3.3 1.8 + - - -
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Residues in contact with LYS 126 (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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124A ARG* 3.1 23.0 + - - +
89B PHE* 4.0 14.8 - - + -
122B LEU 3.0 19.1 + - - +
123B LEU* 3.9 17.0 - - + +
124B ARG 3.5 1.2 - - - -
125B TYR* 1.3 78.6 - - - +
127B GLY* 1.3 82.2 + - - +
128B PRO* 3.9 5.5 + - - +
129B SER* 2.9 19.4 + - - +
131B HIS* 3.5 32.4 - - + +
166B LEU* 3.7 23.2 + - + +
167B ASN* 3.3 37.0 - - - +
168B ASP* 3.8 7.4 - - - +
183B ILE* 4.9 1.3 - - + -
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Residues in contact with GLY 127 (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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124A ARG* 5.3 3.6 - - - -
123B LEU 4.6 3.5 + - - +
124B ARG 4.6 2.6 + - - -
125B TYR 3.3 3.8 + - - -
126B LYS* 1.3 107.1 + - - +
128B PRO* 1.4 71.0 - - - +
129B SER 3.4 1.8 + - - +
168B ASP* 5.9 0.3 - - - +
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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