Contacts of the helix formed by residues 93 - 105 (chain D) in PDB entry 4WFN
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 GLY 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D LYS* 6.2 0.2 - - - -
92D ARG* 1.3 69.9 - - - +
94D GLU* 1.3 67.3 + - - -
95D ARG 3.1 2.9 - - - -
96D MET* 2.9 33.1 + - - +
97D TYR* 3.0 18.6 + - - -
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Residues in contact with GLU 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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5D LYS* 5.4 14.3 - - + +
92D ARG 3.7 0.6 + - - -
93D GLY* 1.3 70.8 - - - -
95D ARG* 1.3 60.2 + - + +
97D TYR* 3.5 10.2 + - - +
98D VAL* 2.9 36.4 + - + +
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Residues in contact with ARG 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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61D THR 4.8 8.8 + - - +
62D LEU* 2.3 42.7 + - - +
63D GLN* 2.9 37.0 + - - +
91D LEU* 4.2 17.8 - - + +
92D ARG 3.6 15.0 - - - +
94D GLU* 1.3 77.2 - - + +
96D MET* 1.3 60.4 + - - +
98D VAL* 3.8 7.0 - - - +
99D PHE* 3.0 30.7 + - - +
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Residues in contact with MET 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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31D ILE* 3.8 25.8 - - - +
32D GLU 4.1 9.2 - - - +
33D LYS* 3.7 26.2 - - - -
34D ILE* 3.9 16.2 - - + +
91D LEU* 3.4 28.9 - - - +
92D ARG 3.8 2.0 + - - -
93D GLY* 2.9 37.3 + - - +
95D ARG* 1.3 80.4 - - - +
97D TYR* 1.3 87.9 + - + +
99D PHE* 3.7 1.7 - - - +
100D LEU* 2.9 32.6 + - + +
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Residues in contact with TYR 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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3D GLN 5.4 2.9 - - - +
4D LEU* 4.3 23.2 - - + +
5D LYS* 3.6 43.5 - - + +
8D TYR* 3.1 45.9 - + + -
31D ILE* 4.7 9.3 + - + +
93D GLY* 3.0 18.2 + - - -
94D GLU* 3.8 8.7 - - - +
96D MET* 1.3 105.3 - - + +
98D VAL* 1.3 59.8 + - + +
100D LEU* 3.8 17.7 - - + +
101D GLU* 2.9 34.4 + - - +
173D MET* 5.8 1.3 - - + -
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Residues in contact with VAL 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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3D GLN* 3.4 33.2 - - + +
60D ILE 5.6 4.0 - - - +
61D THR* 5.9 4.3 - - - +
94D GLU* 2.9 25.2 + - + +
95D ARG* 3.8 7.4 - - - +
96D MET 3.4 0.2 - - - -
97D TYR* 1.3 76.1 - - + +
99D PHE* 1.3 59.1 + - - +
101D GLU* 4.4 2.1 - - - +
102D LYS* 2.9 48.8 + - + +
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Residues in contact with PHE 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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34D ILE* 4.1 19.1 - - + -
36D VAL* 4.1 21.3 - - + -
60D ILE* 4.1 22.9 - - + -
61D THR* 3.6 37.5 - - + +
91D LEU* 3.6 12.1 - - + -
95D ARG 3.0 17.7 + - - +
96D MET 3.7 1.8 - - - +
98D VAL* 1.3 78.6 - - - +
100D LEU* 1.3 68.3 + - - +
102D LYS* 3.0 12.1 + - + +
103D LEU* 2.9 33.4 + - + +
138D PHE* 5.4 6.5 - + - -
152D MET* 4.7 12.1 - - + -
154D ILE* 4.3 20.0 - - + -
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Residues in contact with LEU 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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4D LEU* 5.8 4.0 - - + -
31D ILE* 4.9 18.2 - - + -
34D ILE* 4.8 22.2 - - + -
96D MET* 2.9 23.2 + - + +
97D TYR* 3.8 21.5 - - + +
99D PHE* 1.3 79.4 - - - +
101D GLU* 1.3 57.9 + - + +
103D LEU* 2.9 15.3 + - + +
104D ILE* 2.9 52.6 + - + +
156D ILE* 5.8 6.1 - - + -
173D MET* 5.1 10.8 - - + -
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Residues in contact with GLU 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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3D GLN* 4.8 1.7 - - - -
4D LEU* 3.2 48.2 + - + +
7D LYS* 4.8 8.7 + - - -
97D TYR 2.9 19.7 + - - +
98D VAL* 4.4 1.5 - - - +
100D LEU* 1.3 69.6 - - - +
102D LYS* 1.3 65.6 + - - +
103D LEU 3.0 1.8 - - - -
104D ILE* 4.1 11.0 - - + +
105D ASN* 3.0 56.0 + - + +
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Residues in contact with LYS 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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60D ILE* 4.7 14.7 + - + +
98D VAL* 2.9 37.1 + - + +
99D PHE* 3.0 11.9 + - + +
101D GLU* 1.3 76.4 - - - +
103D LEU* 1.3 55.8 + - - +
106D ILE* 3.1 43.5 - - + +
107D GLY* 3.2 3.5 + - - -
139D PRO* 4.4 14.9 - - + +
140D GLU* 2.3 42.6 + - + +
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Residues in contact with LEU 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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99D PHE* 2.9 24.2 + - + +
100D LEU* 2.9 18.0 + - + +
102D LYS* 1.3 76.5 - - - +
104D ILE* 1.3 64.3 + - + +
107D GLY* 3.0 15.4 + - - +
108D LEU* 2.8 60.7 + - + +
111D ILE* 6.1 0.2 - - + -
130D LEU* 5.4 6.7 - - + -
132D ILE* 4.2 23.3 - - + -
137D ILE* 6.3 2.2 - - + -
138D PHE* 4.8 20.2 - - + -
139D PRO* 6.2 0.4 - - + -
154D ILE* 5.4 8.7 - - + -
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Residues in contact with ILE 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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4D LEU* 6.5 0.2 - - + -
100D LEU* 2.9 45.9 + - + +
101D GLU* 3.2 7.1 + - + +
103D LEU* 1.3 72.5 - - + +
105D ASN* 1.3 69.7 + - - +
108D LEU* 4.2 18.2 - - + +
109D PRO* 3.1 21.5 - - - +
173D MET* 3.1 50.3 - - + +
174D GLY* 4.5 10.5 - - - +
176D PRO* 5.9 2.9 - - + -
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Residues in contact with ASN 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 GLU* 3.0 44.2 + - + +
104D ILE* 1.3 87.8 - - - +
106D ILE* 1.3 68.6 + - + +
109D PRO* 3.1 16.0 - - - +
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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