Contacts of the helix formed by residues 96 - 105 (chain D) in PDB entry 1I4T
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ASP* 6.5 0.4 - - - -
60D GLY 3.8 20.4 + - - -
62D GLU* 4.0 15.0 - - - +
65D ASP* 3.4 36.3 + - - -
68D ARG* 3.9 5.3 - - - +
92D ASN* 2.8 25.0 + - + +
95D ALA* 1.3 76.9 - - + +
97D TRP* 1.3 94.3 - - + +
99D PRO* 3.3 5.6 - - - +
100D GLU* 3.2 26.2 + - + +
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Residues in contact with TRP 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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9D VAL* 4.2 11.9 - - + -
10D GLY* 3.3 26.0 - - - -
11D ASP* 2.4 49.4 - - + +
58D THR* 5.7 0.4 - - - -
59D ALA 4.3 0.2 - - - -
60D GLY* 4.2 11.0 - - - -
68D ARG* 3.2 47.6 - - - -
72D TYR* 4.6 1.1 - - - -
80D ILE* 3.6 25.1 - - + -
81D CYS 4.6 2.5 - - - -
89D SER 5.8 0.2 - - - -
92D ASN* 3.3 22.7 + - + +
93D VAL* 3.8 7.6 - - + +
96D LYS* 1.3 94.0 - - + +
98D TYR* 1.3 68.4 + - - +
100D GLU* 3.0 18.9 + - + -
101D VAL* 3.0 30.0 + - + +
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Residues in contact with TYR 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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80D ILE* 4.0 12.3 - - + +
93D VAL 3.0 22.1 + - - +
94D ARG* 4.1 6.5 - - + -
97D TRP* 1.3 72.3 - - - +
99D PRO* 1.3 79.7 - - + +
101D VAL* 4.2 1.9 - - - +
102D ARG* 3.3 54.2 + - + +
110D ILE* 4.6 4.9 - - + -
148D GLU 5.4 1.7 + - - -
149D ILE* 3.2 66.2 + - + -
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Residues in contact with PRO 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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94D ARG 3.1 27.1 - - - +
95D ALA 4.0 9.0 - - - +
96D LYS 3.3 13.7 - - - +
98D TYR* 1.3 100.2 - - + +
100D GLU* 1.3 55.9 + - - +
102D ARG* 3.7 4.4 - - + +
103D HIS* 2.8 30.3 + - - +
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Residues in contact with GLU 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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65D ASP* 3.2 28.2 - - - +
68D ARG* 3.9 11.5 + - - +
69D PRO* 4.6 7.6 - - - -
72D TYR* 2.8 32.4 + - - -
96D LYS* 3.2 20.8 + - + +
97D TRP* 3.0 14.5 + - + +
99D PRO* 1.3 75.2 - - - +
101D VAL* 1.3 70.0 + - + +
103D HIS* 2.8 24.2 + - + +
104D HIS* 3.2 25.7 + - + +
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Residues in contact with VAL 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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9D VAL* 4.1 26.5 - - + -
72D TYR* 4.7 15.9 - - - +
78D PHE* 3.4 48.8 - - + -
80D ILE* 4.6 7.0 - - + -
97D TRP* 3.0 19.5 + - + +
98D TYR 4.2 2.7 - - - +
100D GLU* 1.3 76.4 + - + +
102D ARG* 1.3 57.8 + - - +
104D HIS* 3.5 2.4 + - - +
105D CYS* 2.8 29.9 + - - +
108D THR* 5.8 0.2 - - - -
110D ILE* 4.3 17.9 - - + -
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Residues in contact with ARG 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 TYR* 3.3 42.2 + - + +
99D PRO* 3.8 4.5 - - + +
100D GLU 3.0 0.8 - - - -
101D VAL* 1.3 74.7 - - - +
103D HIS* 1.3 62.2 + - - +
104D HIS 2.9 7.0 + - - -
105D CYS 3.6 4.2 + - - -
106D PRO* 3.1 39.7 - - + +
107D ASN* 3.1 30.3 - - - +
108D THR 3.0 28.5 + - - +
109D PRO* 4.9 0.8 - - - +
110D ILE* 3.1 32.5 - - + +
149D ILE* 5.4 3.6 - - - +
150D GLY* 5.4 7.7 + - - -
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Residues in contact with HIS 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 PRO 2.8 18.8 + - - +
100D GLU* 2.8 18.4 + - + +
102D ARG* 1.3 70.0 - - - +
104D HIS* 1.3 82.4 + + + +
106D PRO* 4.8 1.9 - - - +
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Residues in contact with HIS 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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69D PRO* 2.9 33.7 - - + +
72D TYR* 3.5 37.5 - + + -
100D GLU* 3.2 28.0 + - + +
101D VAL 4.0 3.6 - - - +
102D ARG 2.9 0.4 - - - -
103D HIS* 1.3 106.4 + + - +
105D CYS* 1.3 67.7 + - - +
106D PRO* 3.3 9.4 - - - +
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Residues in contact with CYS 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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72D TYR* 4.1 24.0 - - - -
73D PRO* 5.0 4.5 - - - -
74D GLN 5.5 0.9 - - - -
75D THR* 5.1 4.0 - - - -
78D PHE* 4.0 18.6 - - + -
101D VAL* 2.8 20.9 + - - +
102D ARG* 3.6 9.7 + - - -
104D HIS* 1.3 85.6 - - - +
106D PRO* 1.3 58.3 - - - +
107D ASN* 3.0 10.0 + - - -
108D THR* 3.3 28.2 + - - +
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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