Contacts of the helix formed by residues 110 - 127 (chain B) in PDB entry 2HOF
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
----------------------------------------------------------
29A ASP* 6.0 0.2 - - - -
68B PRO* 3.1 38.8 - - - +
106B ARG 4.2 1.0 + - - -
107B PRO 3.2 10.5 + - - +
108B SER 3.1 6.1 - - - +
109B ASP* 1.3 80.9 - - - +
111B ASN* 1.3 62.4 + - - +
112B ALA* 3.6 4.4 + - - +
113B VAL 3.3 9.9 + - - -
114B SER* 3.2 18.7 + - - -
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASN* 2.9 27.0 + - - +
29A ASP* 3.6 21.2 + - + +
100A ARG* 4.1 8.0 + - - +
101A ARG* 3.1 61.8 + - - +
103A GLY* 4.7 0.8 - - - +
109B ASP 4.1 1.2 + - - -
110B SER* 1.3 70.2 - - - +
112B ALA* 1.3 59.9 + - - +
114B SER* 4.0 4.0 + - - -
115B LEU* 2.9 43.6 + - + +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 5.0 2.0 - - - -
29A ASP* 3.6 12.7 + - - +
32A ARG* 3.6 14.6 - - - +
33A ASP* 3.6 4.0 - - - +
68B PRO* 4.6 10.8 - - + +
69B GLU* 3.6 26.5 - - - +
72B ARG* 3.5 12.5 - - - -
110B SER* 3.3 9.7 + - - +
111B ASN* 1.3 77.3 - - - +
113B VAL* 1.3 58.3 + - - +
115B LEU* 5.0 0.2 - - - -
116B VAL* 3.3 27.7 + - - +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 3.3 31.6 - - + +
71B VAL* 4.0 15.7 - - + -
72B ARG* 4.2 3.8 - - - +
75B LEU* 4.3 4.0 - - + -
92B LEU* 3.4 34.3 - - + -
107B PRO* 3.2 33.4 - - + +
108B SER* 4.0 5.2 - - - +
110B SER* 3.3 7.2 + - - +
111B ASN 3.2 0.4 - - - -
112B ALA* 1.3 76.6 - - - +
114B SER* 1.3 63.9 + - - +
116B VAL* 3.3 7.8 - - - +
117B MET* 3.1 23.4 + - - +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 5.2 2.4 + - - -
101A ARG* 2.8 31.1 + - - -
92B LEU* 5.9 0.4 - - - -
108B SER* 3.8 20.6 - - - -
110B SER 3.2 15.0 + - - -
111B ASN* 3.8 4.7 + - - -
113B VAL* 1.3 79.0 - - - +
115B LEU* 1.3 60.2 + - - +
117B MET* 3.6 6.0 + - - +
118B ARG* 3.3 26.4 + - - +
19D A 6.0 1.1 - - - -
20D T 5.4 6.7 - - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 3.7 26.0 - - + +
30A MET* 3.8 22.9 - - + +
33A ASP* 3.7 17.9 - - + +
36A ALA* 3.5 16.8 - - + +
37A PHE* 3.5 37.7 - - + -
101A ARG* 3.9 22.9 - - - +
111B ASN* 2.9 33.4 + - + +
114B SER* 1.3 77.8 + - - +
116B VAL* 1.3 63.8 + - - +
118B ARG* 3.4 2.3 + - - -
119B ARG* 3.1 20.8 + - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASP* 3.5 15.2 + - - +
72B ARG* 3.7 31.9 - - + +
75B LEU* 3.8 21.8 - - + -
76B LEU* 3.8 31.2 - - + -
112B ALA 3.3 19.3 + - - +
113B VAL* 3.3 15.0 + - - +
115B LEU* 1.3 77.7 - - - +
117B MET* 1.3 61.7 + - - +
119B ARG* 3.4 4.5 + - - +
120B ILE* 2.8 39.1 + - + +
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Residues in contact with MET 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 4.4 4.9 - - - -
85B VAL* 4.3 9.9 - - + +
88B ILE* 3.9 31.0 - - + -
89B GLN* 3.8 35.9 - - + +
92B LEU* 3.6 30.7 - - + -
113B VAL 3.1 13.5 + - - +
114B SER* 3.8 6.5 - - - +
115B LEU 3.3 0.2 - - - -
116B VAL* 1.3 80.6 - - + +
118B ARG* 1.3 64.5 + - - +
120B ILE* 3.4 14.9 + - + -
121B ARG* 3.0 25.3 + - + +
19D A 4.9 4.9 - - - +
20D T 5.8 2.5 - - - +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 2.8 45.3 + - + +
37A PHE* 3.8 20.1 - - - -
101A ARG* 4.3 13.0 - - - +
114B SER 3.3 14.0 + - - +
115B LEU* 3.7 7.0 - - - +
117B MET* 1.3 76.5 - - - +
119B ARG* 1.3 62.5 + - - +
121B ARG* 3.3 33.2 + - - +
122B LYS* 2.9 29.3 + - - +
22C T 3.4 36.7 + - - -
23C T 3.5 15.0 + - - -
18D T 4.1 15.6 + - - -
19D A 3.9 25.9 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.9 12.8 + - - +
33A ASP* 2.9 30.4 + - + +
34A ARG* 6.1 0.2 - - - +
35A GLN* 3.4 44.1 + - + +
36A ALA* 3.9 9.8 - - + +
72B ARG* 3.5 15.6 - - - +
76B LEU* 4.9 14.9 - - - +
115B LEU 3.1 14.7 + - - +
116B VAL* 3.6 9.2 - - - +
117B MET 3.3 0.2 - - - -
118B ARG* 1.3 79.9 - - - +
120B ILE* 1.3 56.2 + - - +
122B LYS* 3.3 0.7 + - - +
123B GLU* 2.9 62.8 + - - +
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.6 43.1 - - + +
76B LEU* 4.0 15.0 - - + +
79B GLN* 3.9 32.1 - - + +
85B VAL* 4.9 2.7 - - + -
88B ILE* 3.7 30.1 - - + -
116B VAL* 2.8 29.4 + - + +
117B MET* 3.8 15.0 - - + +
118B ARG 3.4 0.2 - - - -
119B ARG* 1.3 71.5 - - + +
121B ARG* 1.3 64.2 + - - +
123B GLU* 5.4 0.7 - - - +
124B ASN* 3.1 28.7 + - - +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.9 26.2 - - + -
89B GLN* 4.7 7.0 - - - +
117B MET* 3.0 14.4 + - + +
118B ARG* 3.5 42.2 + - - +
120B ILE* 1.3 78.8 - - - +
122B LYS* 1.3 79.5 + - - +
124B ASN* 3.9 1.2 - - - +
125B VAL* 3.0 45.2 + - + +
23C T 5.2 0.6 + - - -
18D T 3.5 36.2 + - - -
19D A 2.6 42.7 + - - +
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Residues in contact with LYS 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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35A GLN 3.5 15.5 + - - +
36A ALA 3.1 24.0 - - - +
37A PHE 4.3 0.8 - - - -
38A SER* 4.0 23.7 - - - +
118B ARG* 2.9 20.1 + - - +
119B ARG 3.9 2.7 - - - +
121B ARG* 1.3 95.4 - - - +
123B GLU* 1.3 59.0 + - + +
125B VAL* 4.5 4.5 - - - -
126B ASP* 2.8 49.3 + - - +
23C T 2.7 31.6 + - - -
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Residues in contact with GLU 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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35A GLN* 2.5 35.7 + - + +
76B LEU* 5.7 0.9 - - - +
79B GLN* 3.2 28.1 + - - +
119B ARG* 2.9 49.9 + - + +
120B ILE* 5.4 0.3 - - - +
122B LYS* 1.3 75.2 - - + +
124B ASN* 1.3 61.1 + - - +
126B ASP* 3.9 6.0 - - - +
127B ALA* 3.1 27.7 + - - +
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Residues in contact with ASN 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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79B GLN* 3.1 35.3 + - - +
83B LEU 3.8 16.2 + - - -
85B VAL* 3.5 15.9 - - + +
88B ILE* 4.7 0.2 - - - +
120B ILE* 3.1 17.9 + - - +
123B GLU* 1.3 73.4 - - - +
125B VAL* 1.3 65.1 + - - +
127B ALA* 3.2 12.8 + - - +
128B GLY 3.3 0.7 + - - -
129B GLU* 2.8 51.0 + - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 5.1 6.5 - - + -
121B ARG* 3.0 35.4 + - + +
122B LYS* 4.0 4.7 - - - +
124B ASN* 1.3 75.1 - - - +
126B ASP* 1.3 61.4 + - - +
128B GLY* 2.7 28.1 + - - -
129B GLU* 3.7 17.1 + - + +
130B ARG* 5.0 1.0 + - - -
18D T 6.0 4.3 - - - +
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Residues in contact with ASP 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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122B LYS* 2.8 37.4 + - - +
123B GLU* 3.9 5.8 - - - +
125B VAL* 1.3 79.9 - - - +
127B ALA* 1.3 57.2 + - - +
128B GLY* 3.1 3.3 + - - -
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B GLU 3.1 18.8 + - - +
124B ASN* 3.5 9.2 - - - +
125B VAL 3.2 0.4 - - - -
126B ASP* 1.3 73.4 - - - +
128B GLY* 1.3 60.1 + - - +
129B GLU 3.8 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
------------------------------------------------------------
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