Contacts of the helix formed by residues 98 - 111 (chain B) in PDB entry 4P5E
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 SER 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B SER* 3.8 11.9 - - - -
31B GLY* 4.5 4.3 - - - -
96B GLN 3.4 2.8 + - - -
97B PRO* 1.3 77.5 - - - +
99B LEU* 1.3 62.4 + - - +
101B VAL* 3.0 35.7 + - - +
102B GLY* 3.1 17.8 + - - -
201B N6P 2.6 29.8 + - - -
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Residues in contact with LEU 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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31B GLY* 5.6 0.8 - - - -
98B SER* 1.3 71.5 + - - +
100B GLY* 1.3 58.7 + - - +
102B GLY* 3.3 2.4 + - - -
103B TYR* 2.8 30.1 + - - +
201B N6P 3.9 6.2 + - - +
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Residues in contact with GLY 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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99B LEU* 1.3 77.9 - - - +
101B VAL* 1.3 57.3 + - - +
103B TYR* 3.3 8.8 + - - +
104B GLU* 2.9 34.0 + - - +
201B N6P 2.9 37.8 + - - -
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Residues in contact with VAL 101 (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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26B CYS* 4.0 13.9 - - + -
27B GLY* 3.3 42.6 - - - +
28B SER* 3.5 2.9 - - - +
92B ALA* 4.3 1.8 - - + -
93B GLU 4.5 5.8 - - - +
94B VAL* 4.1 26.9 - - + -
96B GLN 5.5 2.0 - - - +
98B SER* 3.0 22.8 + - - +
100B GLY* 1.3 75.3 - - - +
102B GLY* 1.3 62.6 + - - +
104B GLU* 3.3 9.6 + - - +
105B LEU* 3.0 28.0 + - + +
201B N6P 3.7 4.7 + - + +
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Residues in contact with GLY 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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98B SER 3.1 15.3 + - - -
99B LEU* 3.7 2.9 - - - -
101B VAL* 1.3 75.4 - - - +
103B TYR* 1.3 56.4 + - - +
105B LEU* 3.2 11.3 + - - +
106B GLY* 2.9 26.2 + - - -
131B ILE* 4.8 11.3 - - - +
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Residues in contact with TYR 103 (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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77B HIS* 2.7 41.0 + + - -
81B LEU* 4.1 7.9 - - + -
99B LEU 2.8 17.3 + - - +
100B GLY* 3.5 9.4 - - - +
101B VAL 3.2 0.2 - - - -
102B GLY* 1.3 76.0 - - - +
104B GLU* 1.3 64.8 + - + +
106B GLY* 3.1 2.7 + - - +
107B ARG* 2.9 69.4 + - + +
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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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24B TYR* 2.5 38.0 + - + +
26B CYS* 3.3 24.4 - - - +
80B ASP* 3.8 1.6 - - + +
81B LEU* 6.1 3.6 - - + -
84B LEU* 3.7 14.3 - - + +
100B GLY 2.9 17.5 + - - +
101B VAL* 3.6 4.5 - - - +
103B TYR* 1.3 83.1 - - + +
105B LEU* 1.3 58.1 + - - +
107B ARG* 3.4 0.4 + - - -
108B ALA* 2.8 31.2 + - - +
201B N6P 2.6 54.1 + - + +
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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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26B CYS* 5.1 1.1 - - - -
90B VAL* 4.4 12.1 - - + -
92B ALA* 4.0 13.7 - - + -
94B VAL* 3.9 17.9 - - + -
101B VAL* 3.0 23.9 + - + +
102B GLY* 3.2 7.4 + - - +
104B GLU* 1.3 75.7 - - - +
106B GLY* 1.3 57.0 + - - +
108B ALA* 3.2 3.0 + - - +
109B VAL* 2.9 35.5 + - - +
115B ILE* 3.7 31.8 - - + +
117B CYS* 3.8 23.1 - - - -
131B ILE* 4.0 24.5 - - + -
140B PHE* 4.7 8.3 - - + -
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Residues in contact with GLY 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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102B GLY 2.9 14.2 + - - -
103B TYR* 3.1 3.6 + - - -
105B LEU* 1.3 73.4 - - - +
107B ARG* 1.3 65.5 + - - +
109B VAL* 3.4 7.7 + - - +
110B ALA* 3.1 23.2 + - - +
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Residues in contact with ARG 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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77B HIS* 4.1 5.1 + - - -
81B LEU* 3.5 31.4 - - + +
84B LEU* 3.6 19.1 - - + -
85B GLN* 5.7 0.2 + - - -
103B TYR* 2.9 63.3 + - + +
104B GLU* 4.9 0.2 - - - -
106B GLY* 1.3 75.7 - - - +
108B ALA* 1.3 58.0 + - - +
110B ALA* 3.2 9.2 + - - +
111B PHE* 2.9 54.7 + - + -
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Residues in contact with ALA 108 (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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84B LEU* 3.9 8.0 - - + +
90B VAL* 4.0 26.2 - - + -
104B GLU 2.8 19.0 + - - +
105B LEU* 3.5 7.4 - - - +
106B GLY 3.2 0.2 - - - -
107B ARG* 1.3 74.4 - - - +
109B VAL* 1.3 64.8 + - - +
111B PHE* 3.2 3.3 + - - -
112B ASN 3.1 4.3 + - - -
113B LYS* 3.0 32.3 + - + +
115B ILE* 3.7 17.7 - - + -
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Residues in contact with VAL 109 (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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105B LEU 2.9 21.3 + - - +
106B GLY* 3.8 6.1 - - - +
107B ARG 3.3 0.2 - - - -
108B ALA* 1.3 74.6 - - - +
110B ALA* 1.3 60.2 + - - +
112B ASN* 2.8 23.2 + - - +
113B LYS 4.8 0.4 - - - +
115B ILE* 3.7 5.8 - - + -
134B ALA* 5.1 7.9 - - + +
140B PHE* 3.5 37.0 - - + -
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Residues in contact with ALA 110 (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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106B GLY 3.1 16.1 + - - +
107B ARG* 3.7 11.0 - - - +
109B VAL* 1.3 78.6 - - - +
111B PHE* 1.3 63.4 + - + +
112B ASN* 3.1 2.6 + - - +
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Residues in contact with PHE 111 (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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81B LEU* 3.9 17.3 - - + -
84B LEU* 4.2 16.4 - - + -
85B GLN* 3.3 46.2 - - + -
107B ARG* 2.9 50.5 + - + +
108B ALA* 3.2 6.0 + - - +
110B ALA* 1.3 76.5 - - + +
112B ASN* 1.3 68.1 + - - +
113B LYS* 3.4 24.6 + - + +
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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