Contacts of the helix formed by residues 92 - 112 (chain F) in PDB entry 4PHZ
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 PHE 92 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TRP* 3.6 22.7 - - + +
199E ILE* 3.8 31.4 - - + -
202E TRP* 3.7 27.4 - - + -
203E PHE* 4.1 10.8 - + + -
31F LEU* 4.4 15.3 - - + -
84F TRP* 3.6 47.3 - + - -
90F LEU* 3.0 22.1 + - + -
91F PRO* 1.3 77.6 - - - +
93F GLY* 1.3 59.2 + - - +
96F PHE* 2.8 44.9 + + + +
137F ASP* 3.2 9.9 - - - -
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Residues in contact with GLY 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F SER* 2.6 41.7 + - - -
81F GLN* 3.8 15.0 - - - +
84F TRP* 3.9 7.9 - - - -
90F LEU 4.2 4.0 + - - -
91F PRO 3.7 0.2 - - - -
92F PHE* 1.3 78.2 - - - +
94F ALA* 1.3 62.7 + - - +
96F PHE 3.4 0.2 + - - -
97F ALA* 3.2 13.0 + - - +
137F ASP* 3.1 6.9 + - - -
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Residues in contact with ALA 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F CYS* 3.5 19.9 - - + +
81F GLN* 3.6 13.2 - - - +
93F GLY* 1.3 72.7 - - - +
95F VAL* 1.3 58.2 + - - +
97F ALA 3.3 1.6 + - - -
98F ALA* 2.9 30.7 + - - +
133F ALA* 3.3 28.9 - - - +
136F LEU* 3.9 20.2 - - + -
137F ASP* 2.8 16.0 + - - +
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Residues in contact with VAL 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E GLY* 3.7 36.3 - - - +
198E TRP* 4.0 17.3 - - + +
199E ILE* 4.0 10.1 - - + -
92F PHE 4.2 1.6 - - - +
94F ALA* 1.3 71.0 - - - +
96F PHE* 1.3 64.8 + - - +
98F ALA* 4.5 1.1 - - - +
99F LEU* 2.9 32.3 + - + +
130F ILE* 4.6 5.2 - - + +
133F ALA* 3.7 29.8 - - + -
134F ILE* 3.7 20.9 - - + +
137F ASP* 2.7 23.0 + - - +
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Residues in contact with PHE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ILE* 3.7 20.1 - - + +
31F LEU* 3.5 28.9 - - + -
34F LEU* 3.2 21.5 - - + -
35F PHE* 3.1 53.3 - + - -
38F VAL* 4.0 18.7 - - + +
80F SER* 4.1 4.9 - - - +
84F TRP* 3.6 30.7 - + - +
92F PHE* 2.8 37.0 + + + +
93F GLY* 3.4 5.6 - - - +
95F VAL* 1.3 77.9 - - - +
97F ALA* 1.3 59.4 + - - +
100F GLY* 3.3 16.1 + - - -
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Residues in contact with ALA 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F VAL* 4.2 12.2 - - + +
39F LEU* 5.7 0.2 - - - -
42F TYR* 3.1 35.0 - - + -
76F PHE* 3.5 26.2 - - + +
77F CYS* 3.9 5.4 - - - -
80F SER* 4.0 4.9 - - - -
93F GLY 3.2 8.7 + - - +
94F ALA 3.5 7.6 - - - +
96F PHE* 1.3 78.8 - - - +
98F ALA* 1.3 64.6 + - - +
100F GLY* 3.3 2.8 + - - -
101F LEU 3.1 12.6 + - - -
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F TYR* 3.9 9.6 - - - -
77F CYS* 4.3 7.4 - - - -
94F ALA 2.9 21.6 + - - +
95F VAL* 4.3 1.1 - - - +
97F ALA* 1.3 69.4 - - - +
99F LEU* 1.3 65.6 + - - +
101F LEU* 3.3 4.7 + - - +
102F LEU* 3.0 28.7 + - - +
129F LEU* 4.2 24.2 - - + +
130F ILE* 4.7 3.6 - - + -
133F ALA* 3.6 22.4 - - + -
157F TRP* 5.2 0.2 - - + -
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E MET* 3.7 41.7 - - + +
195E GLY 4.3 0.7 - - - -
196E ALA* 3.8 30.7 - - + +
199E ILE* 3.8 18.4 - - + -
200E PHE* 6.2 0.7 - - + -
35F PHE* 4.4 7.0 - - + -
95F VAL* 2.9 23.9 + - + +
96F PHE 4.4 1.8 - - - +
98F ALA* 1.3 72.7 - - - +
100F GLY* 1.3 67.8 + - - +
102F LEU 3.2 0.7 + - - -
103F ILE* 2.9 45.8 + - + +
130F ILE* 3.9 16.2 - - + +
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Residues in contact with GLY 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PHE* 3.5 26.0 - - - -
38F VAL* 5.8 0.2 - - - -
39F LEU* 2.9 37.3 - - - +
96F PHE 3.3 7.6 + - - -
97F ALA 3.3 7.0 + - - -
98F ALA 3.3 0.6 - - - -
99F LEU* 1.3 77.8 - - - +
101F LEU* 1.3 61.2 - - - +
103F ILE* 3.6 0.7 + - - +
104F GLY 3.1 10.7 + - - -
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 4.2 6.3 - - - -
42F TYR* 3.7 30.9 - - + +
43F HIS* 3.5 43.6 - - + +
46F PHE* 4.0 24.7 - - + -
97F ALA 3.1 12.6 + - - +
98F ALA 3.6 6.1 - - - +
99F LEU 3.2 0.2 - - - -
100F GLY* 1.3 74.1 - - - +
102F LEU* 1.3 60.7 + - - +
104F GLY* 3.0 2.3 + - - -
105F GLU* 2.8 49.1 + - - +
129F LEU* 3.6 31.4 - - + -
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Residues in contact with LEU 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E HIS* 4.6 5.6 - - + +
192E MET* 3.9 20.2 - - + -
98F ALA 3.0 17.1 + - - +
99F LEU 3.8 3.6 - - - +
101F LEU* 1.3 75.5 - - + +
103F ILE* 1.3 57.3 + - - +
105F GLU* 3.3 14.2 + - - +
106F TRP* 2.9 41.5 + - + +
126F PRO* 4.1 14.6 - - + -
127F SER 3.3 21.8 - - - +
128F ALA* 4.7 2.0 - - + -
129F LEU* 3.7 31.6 - - + +
130F ILE* 3.5 29.2 - - + +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E MET* 3.3 24.9 - - + -
196E ALA* 6.3 0.2 - - + -
35F PHE* 4.0 18.8 - - + -
39F LEU* 5.1 6.5 - - + -
99F LEU* 2.9 43.9 + - + +
100F GLY* 3.9 4.5 - - - +
102F LEU* 1.3 72.5 - - - +
104F GLY* 1.3 59.0 + - - +
106F TRP* 4.1 0.8 - - - +
107F ILE* 3.0 49.9 + - + +
119G TYR* 6.0 0.2 - - + -
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Residues in contact with GLY 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F LEU* 3.8 15.7 - - - +
43F HIS* 3.8 5.2 - - - -
100F GLY 3.1 6.9 + - - -
101F LEU 3.0 7.3 + - - -
103F ILE* 1.3 78.7 - - - +
105F GLU* 1.3 61.1 + - - +
107F ILE* 4.1 2.4 + - - +
108F ASN* 3.5 18.0 + - - +
119G TYR* 4.5 9.7 + - - -
123G SER* 3.6 24.3 + - - -
124G PHE* 5.8 0.3 - - - -
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Residues in contact with GLU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F HIS* 3.2 23.4 + - + +
46F PHE* 3.3 26.2 - - - -
54F ASP* 2.7 26.5 - - - +
101F LEU* 2.8 27.6 + - - +
102F LEU* 3.7 16.8 - - - +
104F GLY* 1.3 75.6 - - - +
106F TRP* 1.3 54.2 + - - +
108F ASN* 2.7 8.5 + - - +
109F ARG* 2.7 46.7 + - - +
126F PRO* 3.3 20.1 - - + +
127F SER 4.7 0.9 - - - +
129F LEU* 5.6 0.9 - - - +
127G GLU* 3.7 10.3 - - - +
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Residues in contact with TRP 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E VAL* 3.6 25.4 - - + -
185E TYR* 3.7 29.6 - + - -
188E HIS* 2.9 50.8 + + + +
189E LEU* 4.9 6.7 - - + -
192E MET* 3.6 27.3 - - + -
102F LEU* 2.9 27.4 + - + +
103F ILE* 4.1 2.0 - - - +
105F GLU* 1.3 75.8 - - - +
107F ILE* 1.3 64.3 + - + +
109F ARG* 4.0 7.8 - - + +
110F TYR* 3.0 33.4 + + + +
121F ILE* 3.9 17.7 - - + -
125F PHE* 3.8 9.6 - - + -
126F PRO* 3.4 26.3 - - + +
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Residues in contact with ILE 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ILE* 3.0 42.7 + - + +
104F GLY 4.3 1.1 - - - +
106F TRP* 1.3 76.2 - - - +
108F ASN* 1.3 54.7 + - - +
110F TYR* 4.8 1.8 - - - -
111F VAL* 2.7 47.2 + - + +
119G TYR* 3.5 32.8 - - + +
124G PHE* 4.2 15.7 - - + -
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Residues in contact with ASN 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F GLY 3.5 10.7 + - - +
105F GLU 2.7 11.8 + - - +
107F ILE* 1.3 75.0 - - + +
109F ARG* 1.3 60.3 + - - +
110F TYR 3.0 1.3 - - - -
112F ASN* 2.7 49.9 + - - +
113F PHE* 3.0 24.6 + - - -
123G SER 3.9 0.5 - - - +
124G PHE* 2.9 35.9 - - - +
127G GLU* 3.0 41.5 + - + +
128G GLN* 3.7 2.1 + - - +
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Residues in contact with ARG 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F ASP* 2.6 44.0 + - - +
55F PHE* 3.6 22.2 - - - +
105F GLU* 2.7 31.6 + - - +
106F TRP* 4.0 13.0 - - + +
108F ASN* 1.3 72.2 - - - +
110F TYR* 1.3 58.9 + - - +
113F PHE* 3.2 29.8 + - - +
114F TRP* 3.0 30.8 + - - +
121F ILE* 4.0 5.6 - - + +
124F VAL* 2.7 52.3 + - + +
126F PRO* 3.4 22.5 - - + -
127G GLU* 3.0 31.3 + - - -
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Residues in contact with TYR 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E TYR* 3.7 30.3 - + - -
106F TRP* 3.0 23.6 + + + +
107F ILE* 3.9 2.5 - - - +
109F ARG* 1.3 75.9 - - - +
111F VAL* 1.3 71.9 + - + +
114F TRP* 3.5 26.9 + + - +
115F GLY* 2.8 27.9 + - - -
121F ILE* 4.2 9.2 - - + -
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Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ILE* 2.7 35.0 + - + +
110F TYR* 1.3 86.0 - - + +
112F ASN* 1.3 61.0 + - - +
115F GLY* 3.3 11.6 - - - +
39G ARG* 3.0 39.3 + - + +
124G PHE* 3.8 19.3 - - + -
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Residues in contact with ASN 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ASN* 2.7 48.8 + - - +
110F TYR 3.2 0.4 - - - -
111F VAL* 1.3 76.8 - - - +
113F PHE* 1.3 68.5 + - - +
114F TRP 3.0 1.8 - - - -
116F TRP* 3.0 27.7 + - + +
117F THR* 3.0 5.2 + - - -
39G ARG* 3.0 21.0 + - - -
124G PHE* 3.7 17.2 + - - -
128G GLN* 3.0 45.7 + - + +
131G THR* 4.0 6.4 - - + +
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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