Contacts of the strand formed by residues 113 - 126 (chain H) in PDB entry 3IT8
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 PRO 113 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G HIS* 3.0 35.2 + - + -
75G LEU* 5.7 1.6 - - + -
99G SER* 4.4 0.3 - - - -
65H LYS* 4.6 5.6 - - - -
66H GLY 3.2 7.4 - - - +
67H GLN* 3.0 27.6 - - - +
68H GLY 4.1 0.7 - - - +
111H ALA 4.7 0.4 - - - +
112H LYS* 1.3 94.9 - - + +
114H TRP* 1.3 60.6 + - - +
115H TYR* 4.4 20.7 - - + +
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Residues in contact with TRP 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G HIS* 5.9 0.4 - - + -
99G SER* 3.5 12.1 - - - +
102G GLN* 5.8 8.3 - - + +
64H PHE* 3.8 18.4 - - + -
65H LYS* 3.2 10.1 - - - +
66H GLY* 2.8 53.1 + - - -
68H GLY 3.0 27.7 + - - -
69H CYS* 4.5 2.2 - - - -
70H PRO* 4.8 1.7 - - + +
74H VAL* 5.9 0.4 - - + -
76H LEU* 3.8 22.9 - - + -
100H PRO* 3.7 37.9 - - + -
101H CYS* 3.6 17.7 - - - -
112H LYS 4.8 1.6 - - - -
113H PRO* 1.3 76.5 - - - +
115H TYR* 1.3 74.1 + - - +
116H GLU* 4.1 6.7 - - + +
141H TYR* 3.9 28.0 - + - -
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Residues in contact with TYR 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G LEU* 3.8 40.6 - - + +
97G ILE* 3.5 50.6 - - + +
98G LYS* 3.9 4.8 - - - +
99G SER* 3.2 20.1 + - - +
63H LEU* 4.3 4.9 - - + -
64H PHE 3.4 4.0 - - - +
65H LYS* 3.1 37.1 + - + -
113H PRO* 4.4 15.3 - - + +
114H TRP* 1.3 81.5 - - - +
116H GLU* 1.3 74.2 + - - +
143H LEU* 3.3 33.7 - - + -
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Residues in contact with GLU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G LYS* 3.7 15.1 - - - +
99G SER* 4.8 5.4 + - - +
116G GLU* 5.0 1.4 - - - +
63H LEU* 3.9 1.5 - - - +
64H PHE* 2.9 41.3 + - + +
76H LEU* 4.3 8.7 - - + -
98H LYS* 3.1 53.3 + - + -
99H SER 5.9 0.2 - - - -
100H PRO* 4.4 16.7 - - + +
114H TRP* 4.1 21.4 - - + +
115H TYR* 1.3 83.3 - - - +
117H PRO* 1.3 64.7 - - - +
116I GLU* 5.0 0.9 - - - +
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Residues in contact with PRO 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ALA* 4.0 25.4 - - + -
97G ILE 3.2 22.7 - - - +
98G LYS* 4.2 20.9 - - + +
118G ILE* 5.1 7.6 - - + -
61H GLN* 4.9 7.2 - - - +
62H VAL 3.4 10.5 - - - +
63H LEU* 4.3 7.2 - - + -
98H LYS* 2.9 33.1 + - - +
116H GLU* 1.3 82.2 - - - +
118H ILE* 1.3 67.5 + - - +
117I PRO* 5.7 0.2 - - - +
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Residues in contact with ILE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H GLN* 3.3 8.8 - - - +
62H VAL* 3.0 35.9 + - + -
64H PHE* 3.9 27.1 - - + -
76H LEU 4.3 10.1 - - - +
78H HIS* 3.7 24.9 + - + +
96H ALA* 3.8 31.0 - - + +
97H ILE 4.7 1.3 - - - -
98H LYS* 4.0 31.4 - - + +
116H GLU 4.7 0.2 - - - +
117H PRO* 1.3 81.4 - - - +
119H TYR* 1.3 67.1 + - - +
120H LEU* 4.2 1.3 - - + -
117I PRO* 5.3 6.1 - - + -
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Residues in contact with TYR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 5.8 2.3 - - - +
119G TYR* 3.5 32.6 - + + +
121G GLY* 3.2 37.7 + - - -
59H TYR* 3.5 17.6 - + + +
60H SER 3.6 9.4 - - - -
61H GLN* 4.0 9.4 - - + +
118H ILE* 1.3 76.7 - - - +
120H LEU* 1.3 95.9 + - - +
121H GLY* 4.5 0.9 - - - -
151H TYR* 3.6 22.0 - + - -
61I GLN* 3.3 12.0 + - - -
119I TYR* 3.5 55.1 - + + +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H TYR* 3.0 6.1 - - - +
60H SER 2.9 35.6 + - - +
78H HIS* 3.5 43.3 - - + +
79H THR* 3.8 3.4 - - - -
80H ILE* 4.1 13.5 - - + +
94H LEU* 3.7 34.5 - - + +
95H SER 4.1 5.2 - - - +
96H ALA* 3.7 20.0 - - + -
118H ILE* 4.2 2.9 - - + -
119H TYR* 1.3 93.8 - - - +
121H GLY* 1.3 57.0 + - - +
61I GLN* 3.4 17.9 - - - +
151I TYR* 4.1 3.1 - - - +
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Residues in contact with GLY 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H LEU* 4.9 2.0 - - - -
58H ILE 3.1 12.3 - - - -
59H TYR* 4.0 4.5 - - - -
94H LEU* 3.6 8.5 - - - +
119H TYR* 4.5 0.9 - - - -
120H LEU* 1.3 75.4 - - - +
122H GLY* 1.3 58.2 + - - -
59I TYR* 3.6 1.4 - - - -
119I TYR* 3.2 26.6 + - - -
151I TYR* 3.0 30.0 + - - -
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Residues in contact with GLY 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H LEU* 3.6 7.1 - - - +
58H ILE 2.9 30.7 + - - +
94H LEU* 3.7 5.2 - - - +
121H GLY* 1.3 74.8 - - - -
123H VAL* 1.3 62.8 + - - -
124H PHE* 3.5 19.0 - - - -
15I HIS* 4.3 0.9 - - - -
59I TYR* 3.5 17.7 - - - -
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Residues in contact with VAL 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU* 4.1 17.9 - - + -
56H TYR 3.2 11.4 - - - +
57H LEU* 4.3 9.2 - - + -
122H GLY* 1.3 72.8 - - - +
124H PHE* 1.3 76.3 + - - +
157H LEU* 4.3 11.4 - - + -
13I VAL* 4.0 26.9 - - + -
14I ALA 5.6 0.4 - - - +
15I HIS* 3.7 19.9 - - + +
36I LEU* 4.1 3.4 - - + +
57I LEU* 5.2 0.4 - - + -
59I TYR* 2.8 29.9 + - + +
154I ILE 5.5 0.2 - - - -
155I ILE* 3.9 26.5 - - + -
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Residues in contact with PHE 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLY 3.5 0.9 - - - +
55H LEU* 3.4 6.6 - - - -
56H TYR* 2.8 39.5 + - - +
58H ILE* 4.0 16.8 - - + -
93H LEU* 3.6 46.9 - - + -
94H LEU* 3.7 28.0 - - + -
122H GLY* 3.5 29.4 - - - -
123H VAL* 1.3 88.6 - - - +
125H GLN* 1.3 63.2 + - - +
126H LEU* 3.6 17.4 + - + +
15I HIS* 3.7 17.5 - + - -
34I ASN* 3.6 30.7 - - + -
36I LEU* 4.3 4.0 - - - -
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Residues in contact with GLN 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H GLU* 5.5 2.1 - - - +
54H GLY* 3.5 14.2 + - - +
55H LEU* 3.3 15.8 - - + +
82H ARG* 3.8 14.4 + - - -
124H PHE* 1.3 71.7 - - - +
126H LEU* 1.3 82.4 + - - +
6I ARG* 5.0 16.7 - - - +
7I THR 4.0 2.0 + - - -
8I PRO* 2.9 50.7 + - + +
34I ASN* 5.2 1.7 - - - +
36I LEU* 4.0 25.0 - - + +
160L TYR* 5.6 0.2 + - - -
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Residues in contact with LEU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H VAL* 3.6 29.4 - - + -
52H SER 3.9 0.4 - - - +
53H GLU* 3.3 5.0 - - - +
54H GLY 2.8 32.2 + - - -
56H TYR* 3.8 35.9 - - + -
58H ILE* 4.1 7.9 - - + -
82H ARG* 3.8 20.9 - - - +
93H LEU* 5.1 0.9 - - + -
124H PHE* 3.8 18.2 - - + -
125H GLN* 1.3 93.9 + - - +
127H GLU* 1.3 61.4 + - - +
130H ASP* 3.5 13.0 - - + +
132H LEU* 3.8 19.3 - - + -
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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
------------------------------------------------------------
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