Contacts of the strand formed by residues 94 - 103 (chain D) in PDB entry 1H9D
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 LYS 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ASN* 5.1 0.2 - - - +
49B ARG* 4.8 12.0 - - - +
87D ASP 4.4 3.1 - - - +
88D LEU* 4.4 3.3 - - - +
91D GLU* 2.9 57.5 + - + +
92D ALA 3.9 2.0 - - - +
93D GLY* 1.3 81.8 - - - +
95D VAL* 1.3 59.3 + - - +
96D TYR* 3.3 37.7 + - + -
113D TRP* 3.5 43.6 - - + +
114D ILE 2.9 21.5 - - - +
115D ASP* 3.7 4.0 - - + -
116D LEU* 3.7 9.3 - - - +
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Residues in contact with VAL 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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44D PHE* 4.0 24.0 - - + -
48D CYS* 4.7 4.9 - - + -
86D VAL* 4.3 6.3 - - + -
87D ASP 3.5 18.2 - - - +
88D LEU* 3.9 22.9 - - + -
94D LYS* 1.3 73.5 - - - +
96D TYR* 1.3 72.7 + - - +
97D LEU* 3.9 31.3 + - + +
113D TRP* 3.0 5.4 - - - +
114D ILE* 2.7 41.8 + - + +
116D LEU* 4.0 6.8 - - + +
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Residues in contact with TYR 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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84D GLU 5.6 0.2 - - - +
85D TYR 3.6 1.9 - - - +
87D ASP* 3.0 49.7 + - + +
90D ARG* 3.2 58.2 + - + +
91D GLU* 3.4 21.8 + - + -
94D LYS* 3.3 44.4 + - + -
95D VAL* 1.3 79.4 - - - +
97D LEU* 1.3 63.0 + - - +
112D GLY 3.7 5.2 - - - -
113D TRP* 3.6 25.3 + + + -
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Residues in contact with LEU 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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44D PHE* 4.6 5.6 - - + -
48D CYS* 4.3 7.0 - - - -
55D ILE* 4.5 3.4 - - + -
68D PHE* 3.6 44.6 - - + -
84D GLU 5.6 0.2 - - - -
85D TYR 3.2 11.2 - - - +
86D VAL* 4.2 8.1 - - + -
95D VAL* 3.9 31.9 - - + +
96D TYR* 1.3 83.1 - - - +
98D LYS* 1.3 62.6 + - - +
110D TRP* 3.8 19.1 - - + -
111D LYS* 3.6 5.4 - - - +
112D GLY 2.8 33.5 + - - +
114D ILE* 4.4 17.7 - - + -
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Residues in contact with LYS 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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68D PHE* 3.3 16.1 - - - +
84D GLU* 3.1 44.7 + - + +
85D TYR* 3.0 54.3 + - + -
97D LEU* 1.3 77.6 - - - +
99D ALA* 1.3 60.1 + - - +
100D PRO* 6.5 0.2 - - - -
109D ILE* 3.7 37.2 - - + +
110D TRP 3.4 4.9 - - - -
111D LYS* 4.4 17.5 - - + +
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Residues in contact with ALA 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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66D LEU* 3.9 27.8 - - + -
67D GLN 3.3 18.8 - - - +
68D PHE* 3.7 12.6 - - + -
98D LYS* 1.3 76.8 - - - +
100D PRO* 1.3 68.8 - - - +
101D MET* 3.9 3.9 + - - +
109D ILE* 3.5 2.1 - - - -
110D TRP* 2.8 40.4 + - + +
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Residues in contact with PRO 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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156C PRO* 3.7 14.3 - - + +
157C PRO* 3.7 6.9 - - - +
67D GLN* 3.8 9.0 + - - +
69D PHE 3.1 28.9 - - - +
70D PRO* 4.3 2.5 - - + -
71D ALA* 3.9 22.4 - - + +
85D TYR* 3.9 13.2 - - + +
98D LYS* 6.5 0.2 - - - -
99D ALA* 1.3 86.8 - - - +
101D MET* 1.3 62.6 + - - +
108D VAL 3.5 11.4 - - - +
109D ILE* 4.1 15.7 - - + -
128D ASP* 4.5 6.1 - - - +
131D ARG* 5.6 3.1 - - + +
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Residues in contact with MET 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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156C PRO* 4.0 8.6 - - - +
157C PRO* 3.5 21.5 - - + +
159C VAL* 3.6 18.8 - - + -
64D LEU* 3.2 45.8 - - + -
65D SER 5.3 2.0 - - - +
66D LEU* 4.5 15.3 - - - -
99D ALA* 3.9 7.4 + - - +
100D PRO* 1.3 75.0 - - - +
102D ILE* 1.3 66.0 + - - +
103D LEU* 3.8 28.3 - - + +
107D CYS* 3.8 2.9 - - - +
108D VAL* 3.1 41.2 + - + +
110D TRP* 4.9 3.8 - - - -
125D LEU* 5.3 0.7 - - + -
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Residues in contact with ILE 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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156C PRO* 4.6 2.5 - - + -
157C PRO 2.9 13.2 + - - +
158C GLN* 3.4 13.2 - - + +
159C VAL 2.7 33.6 + - - +
3D ARG* 3.5 58.3 - - + +
4D VAL* 4.0 11.2 - - + -
101D MET* 1.3 74.4 - - - +
103D LEU* 1.3 54.6 + - - +
105D GLY* 3.7 5.2 - - - +
106D VAL 3.7 22.7 - - - +
107D CYS* 4.1 11.9 - - - -
131D ARG* 4.4 7.4 - - - +
135D GLU* 4.0 15.9 - - - +
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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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159C VAL* 3.4 31.6 - - + +
161C THR* 4.6 3.6 - - + -
17D PHE* 3.8 31.9 - - + -
18D PHE* 3.4 8.4 - - + -
62D THR* 6.2 0.2 - - + -
64D LEU* 4.3 7.2 - - + -
101D MET* 3.8 23.5 - - + -
102D ILE* 1.3 70.4 - - - +
104D ASN* 1.3 74.7 + - - +
105D GLY 3.1 0.7 - - - -
106D VAL* 3.1 28.3 + - - +
108D VAL* 4.0 11.0 - - + -
125D LEU* 3.3 37.0 - - + -
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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