Contacts of the helix formed by residues 93 - 107 (chain D) in PDB entry 4H7Y
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 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D GLY 4.1 4.5 - - - -
56D GLN 3.5 26.0 - - - -
57D ASN 3.8 16.8 - - - -
58D GLU* 3.6 34.8 - - + -
61D ALA* 3.6 15.9 - - + -
90D CYS* 3.3 8.5 + - + -
91D LYS 3.1 2.4 + - - -
92D LYS* 1.3 109.6 - - + +
94D ALA* 1.3 66.3 + - - +
95D PHE* 3.7 27.6 - + + -
96D VAL* 3.0 18.8 + - + +
97D HIS* 3.3 14.0 - - - -
126D VAL* 3.7 9.0 - - + -
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LYS 3.6 3.0 + - - -
93D PHE* 1.3 70.3 - - - +
95D PHE* 1.3 62.0 + - - +
97D HIS* 3.1 6.3 + - - +
98D ILE* 3.0 26.6 + - - +
125D ALA* 4.0 10.1 - - - -
126D VAL 2.8 33.5 + - - +
127D PRO* 3.6 17.7 - - + +
130D MET* 4.4 7.9 - - + -
131D LEU* 3.8 21.1 - - + -
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Residues in contact with PHE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU* 4.3 13.5 - - + -
61D ALA* 3.5 25.8 - - + -
62D ARG* 3.7 23.8 - - + -
65D VAL* 3.6 32.3 - - + -
93D PHE* 3.1 35.5 + + + -
94D ALA* 1.3 78.0 - - - +
96D VAL* 1.3 56.2 + - + +
98D ILE* 3.8 5.8 - - - +
99D SER* 3.0 27.7 + - - -
126D VAL 4.7 1.1 + - - -
130D MET* 3.9 26.3 - - + +
146D LEU* 5.9 2.0 - - + -
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ALA* 4.0 8.1 - - + -
65D VAL* 3.6 23.5 - - + +
83D PHE* 5.3 0.6 - - - +
86D ALA* 3.5 39.7 - - + +
87D ARG* 3.7 12.6 - - + +
90D CYS* 3.7 28.5 - - + +
93D PHE* 3.0 21.5 + - + +
95D PHE* 1.3 77.7 - - + +
97D HIS* 1.3 68.2 + - + +
99D SER* 3.4 3.5 + - - -
100D PHE* 3.2 21.3 + - - +
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Residues in contact with HIS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ARG* 3.6 36.6 + - + +
91D LYS* 2.7 34.6 + - + -
93D PHE 3.3 18.2 - - - -
94D ALA* 3.1 6.1 + - - +
96D VAL* 1.3 79.0 - - + +
98D ILE* 1.3 58.3 + - - +
100D PHE* 3.3 7.1 + - - +
101D ALA* 2.8 29.3 + - - +
116D LEU* 4.5 12.8 + - + +
117D LEU* 4.8 1.8 - - + -
119D LYS* 5.7 2.2 - - + +
120D ALA* 3.6 35.6 + - + +
123D ARG* 5.7 7.0 - - + -
125D ALA* 3.8 13.6 - - + +
131D LEU* 4.7 2.7 - - + -
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ALA 3.0 19.4 + - - +
95D PHE* 3.8 5.4 - - - +
96D VAL 3.2 0.2 - - - -
97D HIS* 1.3 74.1 - - - +
99D SER* 1.3 55.3 + - - +
101D ALA* 3.5 6.5 - - - +
102D GLN* 2.6 36.4 + - + +
117D LEU* 3.8 9.4 - - + -
130D MET* 3.4 54.5 - - + +
131D LEU* 3.8 16.4 - - + -
134D ALA* 4.1 2.7 - - + -
145D LEU* 4.2 18.4 - - + -
146D LEU* 4.0 23.6 - - + -
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Residues in contact with SER 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 3.4 15.8 - - - +
69D GLU* 2.9 30.9 + - - +
83D PHE* 3.3 20.1 - - - -
95D PHE 3.0 17.8 + - - -
96D VAL 3.7 4.3 - - - -
97D HIS 3.4 0.2 - - - -
98D ILE* 1.3 76.6 - - - +
100D PHE* 1.3 57.4 + - - +
102D GLN* 3.3 7.5 + - - +
103D PHE* 2.9 28.4 + - - +
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Residues in contact with PHE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ARG* 4.3 9.2 - - + -
83D PHE* 3.5 41.8 - + + +
84D GLN* 3.6 46.9 - - + -
87D ARG* 3.9 28.5 - - + -
96D VAL 3.2 10.8 + - - +
97D HIS* 3.5 10.5 - - - +
99D SER* 1.3 78.9 - - - +
101D ALA* 1.3 62.6 + - - +
103D PHE* 3.1 6.0 + + - +
104D GLU* 3.0 47.3 + - + +
112D LYS* 5.6 3.6 - - - -
116D LEU* 3.6 21.8 - - + -
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D HIS 2.8 21.0 + - - +
98D ILE 3.6 4.0 - - - +
100D PHE* 1.3 74.4 - - - +
102D GLN* 1.3 55.9 + - - +
104D GLU 3.4 0.7 + - - -
105D LEU* 3.0 18.2 + - - +
113D SER* 2.8 31.4 + - - +
116D LEU* 3.8 14.0 - - + +
117D LEU* 3.6 32.5 - - + -
145D LEU* 3.6 7.2 - - + -
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Residues in contact with GLN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 2.6 23.0 + - + +
99D SER* 3.5 9.4 - - - +
101D ALA* 1.3 69.8 - - - +
103D PHE* 1.3 61.9 + - - +
105D LEU* 3.3 5.8 + - - +
106D SER* 2.9 37.0 + - - +
143D LYS 3.4 16.0 + - - +
144D GLN* 3.3 27.2 + - - +
145D LEU* 2.9 42.4 + - + +
146D LEU 4.7 0.5 + - - -
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Residues in contact with PHE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D ALA* 3.9 22.2 - - + -
76D PRO* 3.4 27.6 - - + -
79D ALA* 4.1 1.1 - - + -
80D ARG* 3.9 54.1 - - + -
83D PHE* 3.5 33.2 - + + -
99D SER 2.9 14.0 + - - +
100D PHE* 3.4 11.9 - + - +
102D GLN* 1.3 76.3 - - - +
104D GLU* 1.3 73.6 + - + +
106D SER* 2.6 27.9 + - - -
107D GLN* 3.2 30.4 + - + +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ARG* 2.8 35.2 + - - -
100D PHE* 3.0 34.4 + - + +
101D ALA 3.8 6.1 - - - +
103D PHE* 1.3 78.5 - - - +
105D LEU* 1.3 62.4 + - - +
107D GLN* 3.0 8.8 + - - +
108D GLY 3.2 0.2 + - - -
109D ASN* 2.9 67.5 + - + +
112D LYS* 4.1 17.7 - - + +
113D SER* 4.1 7.4 - - - +
116D LEU* 3.6 17.9 - - + -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA 3.0 17.7 + - - +
102D GLN* 3.5 7.0 - - - +
104D GLU* 1.3 77.2 - - - +
106D SER* 1.3 57.5 + - - +
108D GLY* 3.0 19.3 + - - +
109D ASN 4.5 2.7 - - - +
110D VAL* 3.9 23.5 - - + +
113D SER* 3.7 8.6 - - - +
138D LEU* 3.7 24.0 - - + -
141D GLN* 6.6 0.2 - - - -
142D LYS 3.8 16.8 - - - +
143D LYS* 3.4 26.2 - - - +
145D LEU* 3.8 27.8 - - + -
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLN* 2.9 23.2 + - - +
103D PHE* 2.6 29.0 + - - -
105D LEU* 1.3 77.3 - - - +
107D GLN* 1.3 70.6 + - - +
108D GLY 3.4 0.4 + - - -
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Residues in contact with GLN 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO* 3.6 31.3 + - - +
77D ASP* 3.6 22.4 + - - +
80D ARG* 4.6 4.9 - - - +
103D PHE* 3.3 34.7 - - + +
104D GLU 3.0 8.3 + - - +
106D SER* 1.3 90.9 + - - +
108D GLY* 1.3 61.5 + - - +
109D ASN* 3.7 18.4 + - - +
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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
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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