Contacts of the helix formed by residues 93 - 107 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLY 4.3 4.3 - - - -
56B GLN 3.3 29.6 - - - -
57B ASN 3.8 6.1 - - - -
58B GLU* 3.6 46.7 - - + -
61B ALA* 3.6 15.9 - - + -
90B CYS* 3.3 9.6 + - + -
91B LYS 3.1 2.2 - - - -
92B LYS* 1.3 109.2 - - + +
94B ALA* 1.3 66.5 + - - +
95B PHE* 3.9 21.3 - + + -
96B VAL* 3.1 18.6 + - + +
97B HIS* 3.2 15.8 - - - -
125B ALA* 4.2 0.2 - - - -
126B VAL* 3.7 9.4 - - + +
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LYS 3.6 2.4 + - - -
93B PHE* 1.3 71.2 - - - +
95B PHE* 1.3 58.2 + - - +
97B HIS* 3.1 6.5 + - - +
98B ILE* 2.9 30.2 + - - +
125B ALA* 3.9 10.5 - - - -
126B VAL 2.8 32.0 + - - +
127B PRO* 3.6 17.7 - - + +
130B MET* 4.3 8.5 - - + -
131B LEU* 3.7 20.8 - - + +
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLU* 4.1 24.7 - - + -
61B ALA* 3.6 26.0 - - + -
62B ARG* 3.7 25.8 - - + -
65B VAL* 3.7 33.4 - - + -
93B PHE* 3.1 24.3 + + + -
94B ALA* 1.3 79.3 - - - +
96B VAL* 1.3 58.7 + - + +
98B ILE* 3.9 5.1 - - - +
99B SER* 2.9 30.4 + - - -
127B PRO* 5.6 0.4 - - - +
130B MET* 3.8 25.8 - - + +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 4.0 8.7 - - + +
65B VAL* 3.8 22.1 - - + +
83B PHE* 5.2 1.4 - - - +
86B ALA* 3.6 33.9 - - + +
87B ARG* 3.7 19.1 - - + +
90B CYS* 3.7 29.6 - - + +
93B PHE* 3.1 20.3 + - + +
95B PHE* 1.3 80.8 - - + +
97B HIS* 1.3 62.0 + - + +
99B SER* 3.4 4.2 + - - -
100B PHE* 3.2 20.8 + - - +
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Residues in contact with HIS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.5 37.8 + - + +
91B LYS* 2.8 34.7 + - + -
93B PHE 3.2 24.5 - - - -
94B ALA 3.1 5.7 + - - +
96B VAL* 1.3 79.6 - - + +
98B ILE* 1.3 58.0 + - - +
100B PHE* 3.3 8.7 + - - +
101B ALA* 2.9 28.5 + - - +
116B LEU* 4.6 12.2 + - + +
117B LEU* 4.6 1.5 - - + +
119B LYS* 5.7 1.3 - - + +
120B ALA* 3.5 34.3 + - + +
123B ARG* 5.7 6.7 - - + +
125B ALA* 3.7 15.4 - - + +
131B LEU* 4.6 1.8 - - + -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ALA 2.9 20.6 + - - +
95B PHE* 3.9 5.6 - - - +
96B VAL 3.3 0.2 - - - -
97B HIS* 1.3 74.3 - - - +
99B SER* 1.3 59.7 + - - +
101B ALA* 3.3 1.2 + - - +
102B GLN* 2.7 29.5 + - + +
117B LEU* 3.8 13.2 - - + -
130B MET* 3.4 55.0 - - + +
131B LEU* 3.7 17.0 - - + -
134B ALA* 4.1 6.1 - - + -
145B LEU* 4.2 23.3 - - + -
146B LEU* 4.3 14.8 - - + -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 3.4 15.5 - - - +
69B GLU* 2.8 30.1 + - - +
83B PHE* 3.4 24.0 - - - -
95B PHE 2.9 18.2 + - - -
96B VAL 3.6 5.6 - - - -
97B HIS 3.3 0.2 - - - -
98B ILE* 1.3 76.1 - - - +
100B PHE* 1.3 56.6 + - - +
102B GLN* 3.2 8.4 + - - +
103B PHE* 3.0 23.9 + - - +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 4.3 10.1 - - + -
83B PHE* 3.5 42.0 - + + +
84B GLN* 3.7 40.6 - - + -
87B ARG* 3.9 33.2 - - + -
96B VAL 3.2 10.0 + - - +
97B HIS* 3.5 10.8 - - - +
99B SER* 1.3 77.1 - - - +
101B ALA* 1.3 63.6 + - - +
103B PHE* 3.2 6.0 + + - +
104B GLU* 3.1 45.7 + - + +
112B LYS* 5.3 4.3 - - - -
116B LEU* 3.6 20.9 - - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B HIS 2.9 17.6 + - - +
98B ILE 3.3 2.0 + - - +
100B PHE* 1.3 76.5 - - - +
102B GLN* 1.3 57.5 + - - +
104B GLU 3.4 0.7 + - - +
105B LEU* 2.9 18.9 + - - +
113B SER* 2.8 44.7 + - - +
116B LEU* 3.8 14.5 - - + +
117B LEU* 3.7 12.6 - - + -
145B LEU* 3.5 13.9 - - + -
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 5.1 6.1 - - + +
98B ILE* 2.7 22.3 + - + +
99B SER* 3.4 9.4 - - - +
100B PHE 3.2 0.2 - - - -
101B ALA* 1.3 70.7 - - - +
103B PHE* 1.3 60.4 + - - +
105B LEU* 3.2 7.6 + - - +
106B SER* 2.9 36.6 + - - +
143B LYS 3.5 8.4 + - - -
144B GLN* 2.9 30.2 + - - +
145B LEU* 3.0 38.4 + - + +
146B LEU 4.6 1.4 + - - +
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 3.8 13.9 - - + -
76B PRO* 3.3 29.6 - - + -
79B ALA* 3.9 10.1 - - + -
80B ARG* 3.9 50.7 - - + -
83B PHE* 3.5 40.6 - + + -
99B SER 3.0 7.3 + - - +
100B PHE* 3.2 10.3 + + - +
102B GLN* 1.3 77.1 - - - +
104B GLU* 1.3 73.5 + - + +
106B SER* 2.6 28.6 + - - -
107B GLN* 3.1 33.4 + - + +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 2.5 37.2 + - - -
100B PHE* 3.1 34.8 + - + +
101B ALA 3.9 3.8 - - - +
103B PHE* 1.3 79.5 - - + +
105B LEU* 1.3 60.7 + - - +
107B GLN* 3.1 8.4 + - - +
109B ASN* 2.8 72.6 + - - +
112B LYS* 3.7 28.6 - - + +
113B SER* 4.2 4.9 - - - +
116B LEU* 3.7 9.9 - - + -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA 2.9 18.5 + - - +
102B GLN* 3.4 7.2 - - - +
103B PHE 3.2 0.2 - - - -
104B GLU* 1.3 77.6 - - - +
106B SER* 1.3 57.5 + - - +
108B GLY* 3.0 19.6 + - - -
109B ASN 4.4 2.7 - - - +
110B VAL* 3.7 29.3 - - + +
113B SER* 3.8 7.1 - - - +
138B LEU* 3.8 15.9 - - + -
142B LYS 3.9 11.7 - - - +
143B LYS* 3.2 32.8 - - - +
145B LEU* 4.0 26.9 - - + -
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 4.1 21.5 + - - +
102B GLN* 2.9 22.3 + - - +
103B PHE* 2.6 26.9 + - - -
105B LEU* 1.3 76.4 - - - +
107B GLN* 1.3 74.3 + - - +
108B GLY 3.2 1.0 + - - -
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASP* 6.3 0.6 - - - -
76B PRO* 3.6 33.5 - - - +
77B ASP* 4.1 9.4 - - - +
80B ARG* 4.7 3.6 - - - +
103B PHE* 3.1 40.7 + - + +
104B GLU* 3.6 7.6 - - - +
105B LEU 3.1 1.0 - - - -
106B SER* 1.3 97.8 + - - +
108B GLY* 1.3 60.3 + - - +
109B ASN* 3.3 19.9 + - - +
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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