Contacts of the helix formed by residues 103 - 116 (chain B) in PDB entry 5FQD
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 HIS 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B GLN* 4.7 6.5 - - - +
102B PHE* 1.3 78.9 - - - +
104B PRO* 1.4 80.9 - - + +
105B GLN* 3.3 46.2 + - + +
106B GLU* 3.1 28.2 + - + +
107B VAL* 3.0 21.5 + - - +
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Residues in contact with PRO 104 (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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102B PHE 3.7 5.1 - - - +
103B HIS* 1.4 100.7 - - + +
105B GLN* 1.3 54.0 + - - +
107B VAL* 3.8 7.7 - - + +
108B SER* 3.0 31.1 + - - -
111B ARG* 5.4 0.5 + - - -
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Residues in contact with GLN 105 (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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85B PRO* 5.3 5.6 - - + +
103B HIS* 3.3 25.6 + - + +
104B PRO* 1.3 75.6 - - - +
106B GLU* 1.3 60.4 + - + +
108B SER* 3.9 5.7 - - - -
109B MET* 3.2 27.5 + - - +
175B ASP* 3.0 23.8 + - + +
176B GLY* 3.3 32.8 + - - -
177B ILE* 3.5 23.2 - - + +
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Residues in contact with GLU 106 (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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84B LEU* 4.4 7.9 - - + +
85B PRO* 3.6 31.8 - - + +
86B GLN* 3.0 42.1 + - - +
100B GLN 5.3 0.3 - - - +
101B LEU* 3.9 30.7 - - + +
102B PHE* 3.8 9.2 + - - +
103B HIS* 3.1 31.7 + - + +
105B GLN* 1.3 74.6 - - + +
107B VAL* 1.4 63.1 + - - +
109B MET* 3.4 7.8 + - - +
110B VAL* 3.2 27.2 + - - +
177B ILE* 5.1 2.2 - - - -
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Residues in contact with VAL 107 (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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101B LEU 3.8 21.1 - - - +
102B PHE 4.2 2.5 - - - +
103B HIS 3.0 18.2 + - - +
104B PRO* 3.8 8.3 - - + +
106B GLU* 1.4 71.0 - - - +
108B SER* 1.3 57.9 + - - +
110B VAL* 3.4 5.2 + - - +
111B ARG* 3.0 62.9 + - + +
146B GLU* 5.7 1.3 - - + +
153B GLU* 3.7 28.0 - - + +
154B ILE 5.6 0.2 - - - -
155B VAL* 3.9 25.0 - - + +
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Residues in contact with SER 108 (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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104B PRO 3.0 19.1 + - - -
105B GLN* 3.9 7.0 - - - -
107B VAL* 1.3 73.4 - - - +
109B MET* 1.3 64.0 + - - +
111B ARG* 3.2 19.3 + - - +
112B ASN* 3.1 35.5 + - - +
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Residues in contact with MET 109 (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 PRO* 3.7 29.4 - - + -
83B VAL 3.8 8.5 - - - +
84B LEU* 3.8 30.3 - - + -
105B GLN 3.2 16.6 + - - +
106B GLU* 3.6 4.9 - - - +
107B VAL 3.4 0.2 - - - -
108B SER* 1.3 77.8 + - - +
110B VAL* 1.3 57.6 - - + +
112B ASN* 3.4 13.7 + - + +
113B LEU* 3.1 54.7 + - + +
120B PHE* 4.4 4.9 - - + -
177B ILE* 3.7 37.2 - - + -
179B GLN* 6.1 0.4 - - - +
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Residues in contact with VAL 110 (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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84B LEU* 4.6 12.3 - - + -
101B LEU* 3.4 30.7 - - + -
106B GLU 3.2 11.6 + - - +
107B VAL 3.4 3.3 + - - +
109B MET* 1.3 74.6 - - + +
111B ARG* 1.4 60.5 + - + +
113B LEU* 3.1 12.4 + - + +
114B ILE* 2.9 45.6 + - + +
120B PHE* 5.9 0.4 - - + -
141B ILE* 4.5 13.7 - - + -
144B TYR* 6.3 0.2 - - + -
155B VAL* 4.1 19.3 - - + -
157B VAL* 3.9 24.7 - - + -
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Residues in contact with ARG 111 (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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104B PRO 5.4 0.4 + - - -
107B VAL* 3.0 46.5 + - + +
108B SER* 3.2 23.2 + - - +
110B VAL* 1.4 76.6 - - + +
112B ASN* 1.4 62.3 + - - +
114B ILE* 3.6 9.0 + - - +
115B GLN* 3.0 40.7 + - - +
146B GLU* 3.3 26.9 + - + +
153B GLU* 3.3 33.7 + - - +
155B VAL* 6.3 1.6 - - + -
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Residues in contact with ASN 112 (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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108B SER* 3.1 27.0 + - - +
109B MET* 3.5 12.3 - - + +
110B VAL 3.2 0.2 - - - -
111B ARG* 1.4 76.9 - - - +
113B LEU* 1.4 57.6 + - + +
115B GLN* 3.2 12.8 + - - +
116B LYS* 3.1 58.6 + - - +
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Residues in contact with LEU 113 (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 PRO* 3.7 19.3 - - + -
109B MET* 3.1 40.4 + - + +
110B VAL* 3.1 11.1 + - + +
112B ASN* 1.4 70.5 - - + +
114B ILE* 1.3 60.7 + - - +
115B GLN 3.1 5.2 - - - -
116B LYS* 3.2 16.0 + - + +
117B ASP* 4.2 7.0 - - - +
118B ARG* 2.8 28.9 + - - +
119B THR 3.3 26.2 - - - +
120B PHE* 3.8 19.7 - - + -
141B ILE* 3.8 24.7 - - + -
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Residues in contact with ILE 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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67B PHE* 3.6 38.7 - - + -
110B VAL* 2.9 30.7 + - + +
111B ARG* 3.8 9.0 - - - +
113B LEU* 1.3 75.4 - - - +
115B GLN* 1.4 60.0 + - + +
116B LYS 4.6 0.7 - - - +
118B ARG* 3.9 13.1 - - + +
141B ILE* 3.5 41.3 - - + -
144B TYR* 4.1 28.3 - - + +
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Residues in contact with GLN 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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111B ARG* 3.0 32.2 + - - +
112B ASN* 3.2 14.0 + - - +
113B LEU 3.1 0.6 - - - -
114B ILE* 1.4 80.8 - - + +
116B LYS* 1.4 66.2 + - + +
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Residues in contact with LYS 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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112B ASN* 3.1 45.4 + - - +
113B LEU* 3.2 11.7 + - + +
114B ILE 4.6 0.9 - - - +
115B GLN* 1.4 83.6 - - + +
117B ASP* 1.4 67.8 + - - +
118B ARG* 4.6 6.6 - - - +
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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