Contacts of the helix formed by residues 104 - 115 (chain H) in PDB entry 1W4R
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 ASP 104 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80H LEU* 3.9 14.3 - - + +
81H LEU* 3.0 29.9 + - - +
82H ARG* 2.9 38.3 + - - +
102H PHE* 4.1 2.6 - - - +
103H PRO* 1.3 74.0 - - - +
105H ILE* 1.3 63.2 + - - +
106H VAL 3.2 3.7 + - - -
107H GLU* 3.3 28.8 - - + +
108H PHE* 3.0 24.3 + - + +
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Residues in contact with ILE 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H LEU* 3.6 21.8 - - + -
96H ILE* 4.0 11.4 - - + -
99H GLY* 3.8 32.8 - - - +
100H GLN* 5.9 0.4 - - - -
102H PHE* 3.2 18.2 + - + +
103H PRO 3.4 0.4 - - - -
104H ASP* 1.3 78.3 + - - +
106H VAL* 1.3 68.9 + - + +
108H PHE* 4.0 0.2 - - - +
109H CYS* 3.1 44.1 + - - -
121H VAL* 4.1 6.7 - - + -
135H ALA* 4.0 29.2 - - + +
136H ILE* 4.1 6.5 - - + +
139H LEU* 3.8 18.6 - - + -
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Residues in contact with VAL 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H PRO 5.0 0.6 + - - +
104H ASP 3.3 0.8 - - - -
105H ILE* 1.3 78.5 - - + +
107H GLU* 1.3 75.3 + - - +
109H CYS* 4.2 0.5 - - - +
110H GLU* 3.1 28.4 + - + +
135H ALA* 3.7 19.1 - - + +
138H ASN* 3.6 35.7 - - + +
139H LEU* 4.0 8.3 - - + +
142H LEU* 3.5 27.9 - - + +
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Residues in contact with GLU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H PRO 4.1 5.7 - - - +
104H ASP* 3.3 43.1 - - + +
106H VAL* 1.3 83.3 + - - +
108H PHE* 1.3 62.6 + - + +
110H GLU* 4.0 3.6 - - - +
111H ALA* 3.0 26.7 + - - +
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Residues in contact with PHE 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H ILE* 4.2 13.7 - - + -
81H LEU* 3.7 36.8 - - + -
82H ARG* 4.9 0.9 - - - +
84H VAL 4.9 0.7 - - - -
85H ALA* 3.9 20.6 - - + -
88H ALA* 3.8 15.7 - - + -
94H ILE* 4.1 11.0 - - + -
96H ILE* 3.7 31.0 - - + -
104H ASP* 3.0 19.3 + - - +
105H ILE 4.0 0.2 - - - +
107H GLU* 1.3 79.9 - - + +
109H CYS* 1.3 61.6 + - - +
111H ALA* 3.3 3.9 + - - +
112H MET* 2.9 72.9 + - + +
119H VAL* 4.9 1.6 - - + -
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Residues in contact with CYS 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ILE* 3.7 12.4 - - + +
96H ILE* 3.9 13.7 - - - -
105H ILE* 3.1 30.4 + - - +
108H PHE* 1.3 80.8 - - - +
110H GLU* 1.3 58.5 + - - +
112H MET* 3.8 1.5 - - - +
113H ALA* 2.9 31.9 + - - +
119H VAL* 3.7 28.1 - - + +
121H VAL* 3.8 20.2 - - - -
139H LEU* 3.8 17.9 - - + -
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Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ARG* 2.7 37.6 + - - -
186E ARG* 3.0 19.7 + - - -
190E PHE* 3.5 5.9 - - - -
21H ILE* 4.0 3.2 - - - +
106H VAL* 3.1 19.1 + - + +
107H GLU* 4.1 3.1 - - - +
109H CYS* 1.3 77.4 - - - +
111H ALA* 1.3 57.5 + - - +
113H ALA* 3.8 0.9 - - - +
114H ASN* 2.9 59.1 + - - +
142H LEU* 3.8 24.5 - - + +
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Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H GLU 3.0 19.7 + - - +
108H PHE* 3.8 4.3 - - - +
110H GLU* 1.3 75.8 - - - +
112H MET* 1.3 63.3 + - + +
114H ASN* 3.3 6.9 + - - +
115H ALA* 3.0 30.0 + - - +
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Residues in contact with MET 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H ALA* 3.3 33.9 - - + +
88H ALA* 3.8 6.3 - - + -
89H LEU* 3.8 24.5 - - + -
94H ILE* 3.8 15.7 - - + -
108H PHE* 2.9 55.8 + - + +
111H ALA* 1.3 82.5 - - + +
113H ALA* 1.3 59.2 + - - +
115H ALA* 3.2 8.6 + - - +
117H LYS* 3.0 34.9 + - - +
119H VAL* 3.7 20.2 - - + -
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Residues in contact with ALA 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ARG* 3.6 31.3 - - - +
19H GLY* 3.3 15.6 + - - -
20H GLN 3.8 14.6 - - - +
21H ILE* 3.7 13.7 - - + -
109H CYS 2.9 18.8 + - - +
110H GLU 3.9 0.2 - - - +
112H MET* 1.3 76.1 - - - +
114H ASN* 1.3 59.6 + - - +
116H GLY* 3.0 14.2 + - - -
117H LYS 3.5 10.3 - - - -
119H VAL* 4.0 1.0 - - + +
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Residues in contact with ASN 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E ARG* 2.9 30.0 + - - +
187E LEU* 6.0 3.3 - - - +
190E PHE* 3.5 23.0 - - - -
110H GLU* 2.9 47.6 + - - +
111H ALA* 3.9 5.9 - - - +
112H MET 3.3 0.2 - - - -
113H ALA* 1.3 75.5 - - - +
115H ALA* 1.3 57.4 + - - +
116H GLY 3.3 1.0 + - - -
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H ARG* 5.2 1.2 + - - -
89H LEU* 5.1 11.0 - - + -
111H ALA 3.0 16.1 + - - +
112H MET* 3.5 10.1 - - - +
113H ALA 3.1 0.6 - - - -
114H ASN* 1.3 78.0 - - - +
116H GLY* 1.3 56.3 + - - +
117H LYS* 3.6 17.6 + - + -
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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