Contacts of the helix formed by residues 103 - 121 (chain A) in PDB entry 3JW8
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 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.0 7.0 - - - -
102A ASP* 1.3 72.1 + - - +
104A HIS* 1.4 61.2 + - - +
106A PHE* 3.2 37.3 + + - +
107A VAL* 4.0 4.3 + - + +
133A MSE 3.7 30.5 - - + -
136A ALA* 4.3 2.7 - - + -
137A ILE* 3.5 35.2 - - + -
140A LEU* 3.9 24.0 - - + -
219A PHE* 5.6 0.2 - + - -
222A GLN* 3.0 45.6 + - + +
223A LEU* 4.2 5.6 - - + -
226A ALA* 3.6 29.6 - - + +
229A ARG* 3.9 11.4 - - - +
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 2.9 18.9 + - + +
103A PHE* 1.4 73.9 - - - +
105A VAL* 1.4 65.1 + - - +
107A VAL* 3.1 22.2 + - + +
108A ARG* 2.9 43.0 + - + +
140A LEU* 6.2 0.9 - - + -
144A GLU* 2.8 34.3 + - - -
229A ARG* 3.6 9.3 - - - +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 4.8 1.3 - - - +
36A ASP* 4.1 7.0 - - - +
38A GLN* 5.2 1.1 - - - +
88A VAL* 3.8 28.7 - - + -
100A VAL* 3.7 6.5 - - + -
101A SER* 3.5 22.2 - - - +
102A ASP* 3.0 21.6 + - + +
104A HIS* 1.4 77.2 - - - +
106A PHE* 1.4 57.7 + - - +
108A ARG* 3.4 38.2 + - - +
109A ASP* 2.9 40.1 + - - +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A HIS* 5.1 0.2 + - - -
87A HIS* 3.7 26.4 + + + +
88A VAL* 3.5 41.3 - - + -
90A HIS* 4.4 2.5 - + - -
99A VAL 5.1 0.2 - - - -
100A VAL* 3.8 17.5 - - + -
103A PHE* 3.2 51.0 + + - +
105A VAL* 1.4 77.7 - - - +
107A VAL* 1.3 58.4 + - - +
109A ASP* 3.5 4.9 + - - +
110A VAL* 3.0 32.1 + - - +
133A MSE 4.0 11.4 - - + -
137A ILE* 3.6 25.1 - - + -
219A PHE* 3.8 26.7 - + - -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 4.5 10.1 - - + +
104A HIS* 3.1 33.0 + - + +
106A PHE* 1.3 74.3 - - - +
108A ARG* 1.3 64.8 + - - +
110A VAL* 3.2 4.2 + - - +
111A LEU* 3.0 29.8 + - + +
137A ILE* 4.1 16.4 - - + +
140A LEU* 3.7 34.1 - - + +
141A THR* 3.6 30.5 + - - +
144A GLU* 3.9 9.6 - - - +
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.4 18.6 - - - +
35A ALA* 4.0 25.3 - - + +
36A ASP* 2.8 40.6 + - - +
104A HIS* 2.9 35.0 + - + +
105A VAL* 3.6 25.1 - - - +
107A VAL* 1.3 78.1 - - - +
109A ASP* 1.3 81.4 + - - +
111A LEU* 3.3 9.4 + - - +
112A GLN* 3.0 27.0 + - + +
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 5.1 1.7 - - - +
34A ASN* 2.9 36.1 + - + +
35A ALA 4.4 0.7 + - - -
40A LEU* 3.6 23.7 - - + +
85A HIS* 3.5 13.7 - - - +
88A VAL* 4.5 5.4 + - - +
105A VAL* 2.9 29.4 + - - +
106A PHE* 4.0 4.8 - - - +
108A ARG* 1.3 101.2 + - - +
110A VAL* 1.4 65.9 + - - +
112A GLN* 3.4 9.8 + - - +
113A HIS* 3.2 16.6 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.7 40.6 - - + -
58A SER* 5.4 0.2 - - - -
85A HIS* 3.9 9.4 - - - +
87A HIS* 4.3 7.9 - - + -
106A PHE 3.0 20.7 + - - +
107A VAL 3.2 7.4 + - - +
109A ASP* 1.4 75.3 - - - +
111A LEU* 1.3 58.8 + - - +
113A HIS* 3.3 3.5 + - - +
114A VAL* 2.9 37.3 + - + +
128A LEU* 4.4 4.3 - - + -
137A ILE* 3.6 21.3 - - + -
138A ALA* 6.4 0.4 - - - -
141A THR* 3.9 24.2 - - + +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.0 24.8 + - + +
108A ARG* 3.7 9.6 - - - +
110A VAL* 1.3 71.6 - - - +
112A GLN* 1.3 55.5 + - - +
114A VAL* 3.8 3.8 - - + +
115A ASP* 2.8 43.8 + - - +
141A THR* 3.6 23.8 - - + +
144A GLU* 3.3 36.8 - - + +
145A ARG* 3.8 49.8 - - + +
149A PHE* 4.1 11.4 - - + -
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Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 4.1 19.0 - - + +
33A VAL 2.9 24.6 + - - +
34A ASN* 3.3 27.6 - - - +
35A ALA* 4.0 3.6 + - - +
108A ARG* 3.0 14.0 + - + +
109A ASP* 3.6 11.3 - - - +
110A VAL 3.3 0.2 - - - -
111A LEU* 1.3 77.7 - - - +
113A HIS* 1.3 57.4 + - - +
115A ASP* 3.8 6.2 - - - +
116A SER* 3.0 39.3 + - - +
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Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.7 17.0 - - + +
42A CYS* 3.6 15.7 - - - -
44A TYR* 2.8 35.7 + + - -
56A PHE* 3.7 7.5 - - + -
83A PHE* 3.7 21.7 - + + -
84A ALA 3.4 23.1 - - - -
85A HIS* 2.9 29.8 + - + +
109A ASP 3.2 5.3 + - - +
110A VAL 3.6 6.7 - - - +
112A GLN* 1.3 76.3 - - - +
114A VAL* 1.3 67.3 + - - +
116A SER* 3.3 7.1 + - - -
117A MSE 3.0 26.5 + - + +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.2 10.1 - - + -
83A PHE* 4.0 22.4 - - + -
110A VAL* 2.9 36.1 + - + +
111A LEU* 3.8 6.7 - - - +
113A HIS* 1.3 77.3 - - - +
115A ASP* 1.3 60.5 + - - +
117A MSE 3.3 1.4 + - - +
118A GLN* 2.9 46.9 + - - +
126A VAL* 4.2 11.0 - - + -
128A LEU* 4.6 0.2 - - + -
145A ARG* 5.3 0.9 - - - +
148A HIS* 4.1 5.4 - - + -
149A PHE* 4.0 31.2 - - + -
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU 2.8 27.0 + - - +
112A GLN* 3.8 6.3 - - - +
114A VAL* 1.3 72.4 - - - +
116A SER* 1.4 62.4 + - - +
118A GLN* 3.4 14.1 + - - +
119A LYS* 3.2 23.0 + - - +
145A ARG* 2.7 44.6 + - - -
148A HIS* 4.7 0.3 + - - -
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 6.0 1.1 - - - +
112A GLN* 3.0 25.5 + - - +
113A HIS* 3.8 11.2 - - - -
115A ASP* 1.4 76.7 - - - +
117A MSE 1.4 61.6 + - - +
119A LYS* 3.5 23.5 + - - +
120A ASP* 3.4 26.8 + - - +
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Residues in contact with MSE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 3.9 24.0 - - + -
54A LEU* 4.2 10.3 - - + -
81A LEU* 3.6 31.4 - - + -
83A PHE* 3.4 43.3 - - + -
113A HIS* 3.0 19.6 + - + +
114A VAL 3.8 1.3 - - - +
116A SER* 1.4 75.9 - - - +
118A GLN* 1.3 63.7 + - - +
120A ASP* 3.3 13.4 + - - +
121A TYR* 3.0 56.0 + - + +
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.1 6.3 - - + -
114A VAL* 2.9 25.3 + - + +
115A ASP* 3.9 10.7 - - - +
116A SER 3.4 0.4 - - - -
117A MSE 1.3 77.4 - - - +
119A LYS* 1.3 60.9 + - - +
121A TYR 3.2 7.0 - - - +
122A PRO* 3.2 26.9 - - - +
123A GLY 6.1 0.4 - - - +
124A LEU 4.0 9.3 + - - +
126A VAL* 3.1 36.4 - - + +
148A HIS* 2.9 36.5 + - - -
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP 3.2 16.2 + - - +
116A SER* 3.6 19.9 + - - +
117A MSE 3.3 0.2 - - - -
118A GLN* 1.3 73.7 - - - +
120A ASP* 1.3 73.7 + - - +
122A PRO* 3.5 14.0 - - - +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.4 15.0 + - - +
117A MSE 3.3 14.6 + - - +
119A LYS* 1.3 91.5 - - - +
121A TYR* 1.4 84.4 + - + +
122A PRO* 3.5 5.7 - - - +
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Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS* 3.0 37.0 + - - +
51A PRO* 4.0 20.2 - - + -
54A LEU* 4.2 11.1 - - + +
81A LEU* 3.3 24.1 - - + +
117A MSE 3.0 36.9 + - + +
118A GLN* 3.2 10.4 - - - +
120A ASP* 1.4 95.1 - - + +
122A PRO* 1.4 68.7 - - - +
123A GLY 3.5 0.2 + - - -
124A LEU* 3.4 31.3 + - + +
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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
------------------------------------------------------------
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