Contacts of the helix formed by residues 110 - 127 (chain B) in PDB entry 5TWF
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 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU* 3.9 26.3 - - - +
84B CYS 4.1 0.2 - - - -
85B PRO* 3.1 15.2 + - - -
109B CYS* 1.3 77.2 - - - +
111B ALA* 1.3 61.8 + - - +
112B PRO* 3.8 12.2 - - - +
113B LYS* 3.0 25.5 + - - +
114B TYR* 2.8 27.8 + - - +
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Residues in contact with ALA 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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72B TYR* 4.5 0.4 - - - -
84B CYS* 3.0 23.7 + - + +
85B PRO 4.0 1.8 + - - -
86B VAL 4.2 4.4 - - - +
87B MET* 3.5 27.1 - - + +
109B CYS 3.7 2.0 + - - -
110B SER* 1.3 69.5 - - - +
112B PRO* 1.3 67.1 - - + +
114B TYR* 3.3 0.9 + - - +
115B ILE* 2.9 30.0 + - - +
161B HIS* 3.6 30.5 - - + +
301B ZN 4.0 0.7 - - - -
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Residues in contact with PRO 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.8 13.1 - - - +
79B CYS* 3.7 18.2 - - + +
80B THR* 3.5 30.3 - - - +
81B GLU* 3.8 2.7 - - + +
84B CYS 3.5 9.6 - - - +
110B SER* 3.6 9.4 - - - +
111B ALA* 1.3 93.9 - - + +
113B LYS* 1.3 61.6 + - - +
115B ILE* 4.0 0.7 - - - +
116B ASP* 3.0 24.4 + - - +
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Residues in contact with LYS 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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109B CYS* 4.2 7.6 - - + -
110B SER* 3.0 29.1 + - - +
112B PRO* 1.3 77.3 - - - +
114B TYR* 1.3 53.9 + - - +
116B ASP* 2.9 7.8 + - - +
117B TYR* 2.7 57.2 + - + -
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Residues in contact with TYR 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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87B MET* 3.5 35.2 - - + -
95B TYR* 3.3 39.2 - - + +
96B HIS 3.8 5.8 + - - -
97B TRP* 3.8 34.3 - + + -
109B CYS* 4.2 11.6 - - - -
110B SER 2.8 14.9 + - - +
113B LYS* 1.3 70.9 - - - +
115B ILE* 1.3 70.4 + - + +
117B TYR* 3.0 11.7 + - - +
118B LEU* 2.9 47.2 + - + +
157B ARG* 2.6 41.7 + - + -
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.8 48.5 - - + +
87B MET* 3.9 26.2 - - + -
111B ALA* 2.9 26.6 + - + +
112B PRO 4.0 2.9 - - - +
114B TYR* 1.3 79.8 - - + +
116B ASP* 1.3 58.0 + - - +
118B LEU* 3.3 3.2 + - + +
119B MET* 2.8 51.6 + - + +
157B ARG* 6.0 0.2 - - + -
158B VAL* 4.1 33.4 - - + -
161B HIS* 5.2 3.1 - - + -
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Residues in contact with ASP 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 PRO 3.0 14.1 + - - +
113B LYS* 2.9 11.5 + - - +
115B ILE* 1.3 76.4 - - - +
117B TYR* 1.3 64.1 + - + +
119B MET* 4.0 4.3 - - - +
120B THR* 2.8 41.5 + - - -
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Residues in contact with TYR 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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97B TRP* 3.1 50.4 + + + +
103B ILE* 4.5 13.5 - - + -
107B ILE* 5.4 8.0 - - + +
109B CYS* 4.9 10.4 - - - +
113B LYS* 2.7 51.4 + - + +
114B TYR* 3.1 11.0 - - - +
116B ASP* 1.3 76.2 - - + +
118B LEU* 1.3 59.1 + - - +
120B THR* 3.4 4.6 + - - -
121B TRP* 2.9 24.9 + - - +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP* 3.3 27.8 - - + -
114B TYR* 2.9 39.4 + - + +
115B ILE* 4.0 7.0 - - + +
117B TYR* 1.3 74.6 - - - +
119B MET* 1.3 81.2 + - + +
121B TRP* 3.3 0.8 - - + +
122B VAL* 2.7 43.3 + - + +
154B ARG* 3.5 37.5 - - + +
155B LEU* 3.9 16.6 - - + -
157B ARG* 5.1 0.9 - - + -
158B VAL* 4.2 11.7 - - + -
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.4 36.5 - - + +
68B ILE* 4.5 7.2 - - + -
69B ASN* 3.4 53.8 - - + +
72B TYR* 6.1 1.1 - - + -
115B ILE* 2.8 42.6 + - + +
116B ASP* 4.0 4.7 - - - +
118B LEU* 1.3 97.2 - - - +
120B THR* 1.3 57.8 + - - +
123B GLN* 3.0 28.8 + - - +
155B LEU* 4.3 5.2 - - - -
158B VAL* 4.8 4.7 - - + -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 2.8 31.3 + - - -
117B TYR* 3.7 3.6 - - - -
119B MET* 1.3 73.2 - - - +
121B TRP* 1.3 56.8 + - - +
123B GLN* 3.5 7.4 - - + +
124B ASP* 2.7 52.8 + - - +
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Residues in contact with TRP 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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97B TRP* 3.8 16.6 - + + -
99B ASP* 4.0 33.9 + - + +
101B THR* 6.3 1.2 - - - +
117B TYR 2.9 15.1 + - - +
118B LEU* 3.1 13.2 + - + +
120B THR* 1.3 76.7 - - - +
122B VAL* 1.3 80.4 + - + +
124B ASP* 3.2 11.1 + - + +
125B GLN* 2.9 65.6 + - + +
147B VAL* 5.1 2.2 - - + -
150B THR* 4.3 12.8 - - + -
151B ILE* 3.7 31.4 - - + -
154B ARG* 4.1 34.3 - - - -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 5.8 0.2 - - + -
65B PHE* 3.4 36.3 - - + -
118B LEU* 2.7 26.8 + - + +
121B TRP* 1.3 87.6 - - + +
123B GLN* 1.3 57.2 - - - +
125B GLN* 3.2 8.7 + - - +
126B LEU* 2.9 33.7 + - + +
151B ILE* 3.6 37.7 - - + +
154B ARG* 5.5 1.6 - - + -
155B LEU* 3.9 16.6 - - + -
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Residues in contact with GLN 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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65B PHE* 4.1 23.7 - - + -
69B ASN* 5.7 1.2 + - - -
119B MET 3.0 19.3 + - - +
120B THR* 3.5 10.1 - - + +
121B TRP 3.2 0.2 - - - -
122B VAL* 1.3 77.2 - - - +
124B ASP* 1.3 58.8 + - - +
126B LEU* 2.8 28.9 + - - +
127B ASP* 2.9 36.4 + - - +
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Residues in contact with ASP 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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120B THR* 2.7 41.8 + - - +
121B TRP* 3.5 9.0 - - + +
123B GLN* 1.3 73.0 - - - +
125B GLN* 1.3 66.4 + - - +
127B ASP* 2.8 31.9 + - - +
128B ASP* 4.1 3.1 - - - +
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Residues in contact with GLN 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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121B TRP* 2.9 70.0 + - + +
122B VAL* 3.3 8.5 - - - +
123B GLN 3.2 0.2 - - - -
124B ASP* 1.3 81.7 - - - +
126B LEU* 1.3 60.3 + - - +
128B ASP* 3.8 11.4 + - - +
131B LEU* 3.8 18.2 - - - +
132B PHE* 3.0 21.1 - - + -
147B VAL* 3.8 22.8 - - + +
151B ILE* 3.7 18.6 - - + -
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Residues in contact with LEU 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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61B THR* 5.2 2.9 - - + -
62B VAL* 3.9 37.0 - - + -
65B PHE* 3.7 35.7 - - + -
122B VAL* 2.9 24.1 + - + +
123B GLN* 2.8 17.0 + - - +
125B GLN* 1.3 75.3 - - - +
127B ASP* 1.3 64.4 + - - +
128B ASP 3.5 3.5 + - - -
132B PHE* 3.6 46.2 - - + +
151B ILE* 4.8 2.0 - - + -
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Residues in contact with ASP 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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123B GLN* 2.9 35.4 + - - +
124B ASP* 2.8 18.8 + - - +
126B LEU* 1.3 82.9 - - - +
128B ASP* 1.3 60.7 + - - +
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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