Contacts of the helix formed by residues 92 - 112 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198I TRP* 3.6 22.9 - - + +
199I ILE* 3.8 30.7 - - + -
202I TRP* 3.6 28.5 - - + -
203I PHE* 4.1 9.6 - + + -
31J LEU* 4.3 14.6 - - + -
84J TRP* 3.7 29.2 - + + -
90J LEU* 3.1 33.5 + - + -
91J PRO* 1.3 78.9 - - - +
93J GLY* 1.3 57.3 + - - +
94J ALA 3.4 2.5 - - - -
96J PHE* 2.8 64.2 + + + +
137J ASP* 3.5 6.1 - - - -
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Residues in contact with GLY 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J SER* 2.5 32.1 + - - -
81J GLN* 3.8 21.3 - - - +
84J TRP* 3.8 14.1 - - - +
90J LEU 4.2 4.0 + - - -
91J PRO 3.6 0.2 - - - -
92J PHE* 1.3 79.6 - - - +
94J ALA* 1.3 61.8 + - - +
96J PHE* 3.4 0.5 - - - +
97J ALA* 3.3 9.5 + - - +
137J ASP* 3.2 4.8 + - - -
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Residues in contact with ALA 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77J CYS* 3.3 21.3 - - + -
81J GLN* 3.5 13.9 - - - +
93J GLY* 1.3 72.6 - - - +
95J VAL* 1.3 56.0 + - - +
97J ALA 3.4 0.7 + - - -
98J ALA* 2.9 30.7 + - - +
133J ALA* 3.5 22.0 - - - +
136J LEU* 3.8 20.2 - - + -
137J ASP* 2.9 23.2 + - - +
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Residues in contact with VAL 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I GLY* 3.7 36.8 - - - +
198I TRP* 4.1 18.8 - - + +
199I ILE* 4.2 7.6 - - + -
92J PHE 4.2 1.1 - - - +
94J ALA* 1.3 70.0 - - - +
96J PHE* 1.3 67.8 + - - +
97J ALA 3.2 0.4 - - - -
98J ALA* 4.4 1.1 - - - +
99J LEU* 2.8 33.3 + - + +
130J ILE* 4.8 6.7 - - + +
133J ALA* 3.8 7.9 - - + +
134J ILE* 3.8 39.3 - - + +
137J ASP* 2.7 22.8 + - - +
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Residues in contact with PHE 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199I ILE* 3.7 20.3 - - + +
31J LEU* 3.6 28.5 - - + -
34J LEU* 3.3 22.4 - - + -
35J PHE* 3.1 49.9 - + + -
38J VAL* 3.9 16.7 - - + +
80J SER* 4.1 6.5 - - - +
84J TRP* 3.6 29.2 - + - +
92J PHE* 2.8 40.3 + + + +
93J GLY 3.4 5.2 - - - +
95J VAL* 1.3 79.1 - - - +
97J ALA* 1.3 60.5 + - - +
100J GLY* 3.3 13.5 + - - -
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Residues in contact with ALA 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J VAL* 4.1 15.1 - - + +
42J TYR* 3.1 29.0 - - + -
76J PHE* 3.7 26.0 - - + +
77J CYS* 4.1 2.2 - - - -
80J SER* 4.0 6.1 - - - -
93J GLY 3.3 9.0 + - - +
94J ALA 3.8 5.8 - - - +
95J VAL 3.2 0.2 - - - -
96J PHE* 1.3 78.5 - - - +
98J ALA* 1.3 65.4 + - - +
100J GLY* 3.2 2.4 + - - -
101J LEU 3.1 17.7 + - - -
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Residues in contact with ALA 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J TYR* 4.0 8.9 - - - -
77J CYS* 4.2 7.6 - - - -
94J ALA 2.9 21.0 + - - +
95J VAL* 4.2 1.8 - - - +
97J ALA* 1.3 72.8 - - - +
99J LEU* 1.3 57.7 + - - +
101J LEU* 3.3 4.2 + - - +
102J LEU* 3.0 34.2 + - - +
129J LEU* 4.2 23.3 - - + +
130J ILE* 4.7 3.6 - - + -
133J ALA* 3.6 22.4 - - + -
157J TRP* 5.3 0.2 - - + -
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Residues in contact with LEU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I MET* 3.7 44.0 - - + +
195I GLY* 4.9 0.7 - - - -
196I ALA* 3.6 34.8 - - + +
199I ILE* 4.1 14.4 - - + -
200I PHE* 6.1 0.9 - - + -
35J PHE* 4.5 8.1 - - + -
95J VAL* 2.8 27.3 + - + +
96J PHE 4.4 1.6 - - - +
98J ALA* 1.3 70.6 - - - +
100J GLY* 1.3 66.7 + - - +
102J LEU 4.5 0.2 - - - +
103J ILE* 3.0 45.0 + - + +
130J ILE* 3.9 12.2 - - + +
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Residues in contact with GLY 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J PHE* 3.6 23.9 - - - -
38J VAL* 5.8 0.4 - - - -
39J LEU* 2.9 38.7 - - - +
96J PHE 3.3 7.4 + - - -
97J ALA 3.2 7.8 + - - -
99J LEU* 1.3 81.2 - - - +
101J LEU* 1.3 60.3 + - - +
103J ILE* 3.5 1.2 + - - +
104J GLY 3.1 9.2 + - - -
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Residues in contact with LEU 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J LEU* 4.2 7.1 - - - +
42J TYR* 3.7 30.2 - - + +
43J HIS* 3.5 44.4 - - + +
46J PHE* 4.1 23.3 - - + -
97J ALA 3.1 13.0 + - - +
98J ALA 3.5 5.4 - - - +
99J LEU 3.1 0.2 - - - -
100J GLY* 1.3 72.9 - - - +
102J LEU* 1.3 67.3 + - - +
104J GLY* 3.0 1.9 + - - -
105J GLU* 2.8 43.9 + - - +
129J LEU* 3.6 29.8 - - + -
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Residues in contact with LEU 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I HIS* 4.5 7.6 - - + +
192I MET* 4.1 20.9 - - + -
98J ALA 3.0 18.2 + - - +
99J LEU 3.3 3.8 + - - +
101J LEU* 1.3 77.3 - - - +
103J ILE* 1.3 57.0 + - - +
105J GLU* 3.3 14.3 + - - +
106J TRP* 2.9 39.6 + - + +
126J PRO* 4.1 14.1 - - + -
127J SER 3.4 23.3 - - - +
128J ALA* 4.8 1.6 - - + -
129J LEU* 3.8 30.5 - - + +
130J ILE* 3.2 31.6 - - + +
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Residues in contact with ILE 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192I MET* 3.4 24.7 - - + -
196I ALA* 6.4 0.2 - - + -
35J PHE* 4.0 18.2 - - + -
36J PHE* 6.5 0.2 - - + -
39J LEU* 5.1 8.1 - - + -
99J LEU* 3.0 42.3 + - + +
100J GLY* 3.8 3.4 - - - +
102J LEU* 1.3 74.7 - - - +
104J GLY* 1.3 58.4 + - - +
106J TRP* 4.5 1.3 - - - -
107J ILE* 2.8 52.1 + - + +
119K TYR* 5.8 0.4 - - + -
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Residues in contact with GLY 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J LEU* 3.7 13.0 - - - -
43J HIS* 3.7 4.8 - - - -
100J GLY 3.1 7.7 + - - -
101J LEU 3.0 6.8 + - - -
103J ILE* 1.3 75.8 - - - +
105J GLU* 1.3 60.3 + - - +
107J ILE* 4.3 2.3 - - - +
108J ASN* 3.4 21.0 + - - +
119K TYR* 4.4 13.1 + - - -
123K SER* 3.6 25.2 + - - -
124K PHE* 5.7 0.3 - - - -
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Residues in contact with GLU 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J HIS* 3.4 19.9 - - + +
46J PHE* 3.3 25.8 - - - -
54J ASP* 2.7 23.8 - - - +
101J LEU* 2.8 31.0 + - - +
102J LEU* 3.6 12.1 - - - +
104J GLY* 1.3 74.5 - - - +
106J TRP* 1.3 54.3 + - - +
108J ASN* 2.8 8.1 + - - +
109J ARG* 2.7 44.6 + - - +
126J PRO* 3.3 22.3 - - + +
127J SER 4.8 1.2 - - - +
129J LEU* 5.6 0.9 - - - +
127K GLU* 3.4 14.1 - - - +
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Residues in contact with TRP 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I VAL* 3.8 16.2 - - + -
185I TYR* 3.7 29.6 - + - -
188I HIS* 3.0 48.4 + + + +
189I LEU* 4.9 7.9 - - + -
192I MET* 3.6 27.5 - - + -
102J LEU* 2.9 30.6 + - + +
103J ILE* 4.0 2.5 - - - +
105J GLU* 1.3 68.8 - - - +
107J ILE* 1.3 69.0 + - + +
109J ARG* 4.0 9.6 - - + +
110J TYR* 3.0 32.7 + - + +
121J ILE* 3.9 17.0 - - + -
125J PHE* 3.8 18.8 - - + -
126J PRO* 3.5 25.9 - - + +
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Residues in contact with ILE 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103J ILE* 2.8 46.3 + - + +
104J GLY 4.3 1.1 - - - +
106J TRP* 1.3 72.5 - - - +
108J ASN* 1.3 59.0 + - - +
110J TYR* 4.8 2.7 - - - -
111J VAL* 2.7 39.9 + - + +
119K TYR* 3.3 33.7 - - + +
124K PHE* 4.1 19.5 - - + -
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Residues in contact with ASN 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J GLY 3.4 12.4 + - - +
105J GLU 2.8 11.8 + - - +
107J ILE* 1.3 75.9 - - + +
109J ARG* 1.3 57.5 + - - +
112J ASN* 2.7 46.6 + - - +
113J PHE* 3.1 23.3 + - - -
123K SER 3.9 0.2 - - - +
124K PHE* 2.8 36.5 - - - +
127K GLU* 3.0 42.2 + - - +
128K GLN 3.6 1.6 + - - +
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Residues in contact with ARG 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J GLY 5.2 0.2 + - - -
54J ASP* 2.9 41.5 + - - +
55J PHE* 3.5 21.1 - - - +
105J GLU* 2.7 32.3 + - - +
106J TRP* 4.0 12.8 - - + +
108J ASN* 1.3 71.7 - - - +
110J TYR* 1.3 57.3 - - - +
113J PHE* 3.1 24.2 + - - +
114J TRP* 2.9 31.2 + - - +
121J ILE* 3.9 5.7 - - + +
124J VAL* 2.7 52.6 + - + +
126J PRO* 3.2 27.2 - - + +
127K GLU* 2.9 35.9 + - - -
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Residues in contact with TYR 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I TYR* 3.8 28.0 - + - -
106J TRP* 3.0 23.6 + + + +
107J ILE* 3.9 2.7 - - - +
109J ARG* 1.3 75.3 - - - +
111J VAL* 1.3 73.4 + - + +
114J TRP* 3.5 26.3 + + - +
115J GLY* 2.9 27.0 + - - -
121J ILE* 4.2 9.4 - - + +
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Residues in contact with VAL 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J ILE* 2.7 34.7 + - + +
110J TYR* 1.3 84.1 - - + +
112J ASN* 1.3 68.3 - - - +
115J GLY* 3.3 11.9 - - - -
39K ARG* 2.9 33.0 + - + +
124K PHE* 3.8 20.6 - - + -
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Residues in contact with ASN 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ASN* 2.7 47.4 + - - +
110J TYR 3.3 0.2 - - - -
111J VAL* 1.3 76.3 - - - +
113J PHE* 1.3 68.6 + - - +
114J TRP 3.0 1.3 - - - -
116J TRP* 2.9 23.3 + - + +
117J THR* 3.0 9.5 + - - -
39K ARG* 3.0 27.4 + - - -
124K PHE* 3.7 21.4 + - - -
128K GLN* 3.0 36.7 + - + +
131K THR* 4.0 6.7 - - + +
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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
------------------------------------------------------------
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