Contacts of the strand formed by residues 54 - 67 (chain I) 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 GLY 54 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7G THR 5.5 1.3 + - - -
8G PRO 4.5 3.4 - - - -
9G SER* 6.0 0.7 - - - -
52I SER 3.6 0.6 + - - -
53I GLU* 1.3 76.0 - - - +
55I LEU* 1.3 60.5 + - - -
56I TYR* 3.4 13.3 - - - -
125I GLN* 3.5 17.0 + - - +
126I LEU 2.8 37.0 + - - -
156I ALA* 6.5 0.4 - - - -
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Residues in contact with LEU 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G PRO* 3.6 8.9 + - + +
9G SER* 3.1 30.4 - - - +
11G LYS* 4.7 1.6 - - + +
13G VAL* 3.9 22.9 - - + -
36G LEU* 4.2 14.1 - - + -
155G ILE* 3.9 13.7 - - + -
54I GLY* 1.3 72.7 - - - -
56I TYR* 1.3 63.6 + - - +
123I VAL* 4.1 17.3 - - + -
124I PHE 3.4 1.8 - - - +
125I GLN* 3.4 40.6 - - + +
156I ALA* 3.7 2.6 - - - +
157I LEU* 3.0 42.1 + - + +
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Residues in contact with TYR 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I PRO* 3.7 16.9 - - + +
50I VAL* 3.0 33.5 - - + +
51I PRO* 3.8 2.5 - - + +
52I SER* 3.0 34.7 + - - -
53I GLU 4.6 0.4 - - - -
54I GLY* 3.4 25.4 - - - -
55I LEU* 1.3 76.5 - - - +
57I LEU* 1.3 61.4 + - - +
58I ILE* 3.6 10.4 + - + +
123I VAL* 3.2 7.4 - - - +
124I PHE* 2.8 34.4 + - - +
126I LEU* 3.8 26.5 - - + -
154I ILE* 4.0 21.1 - - + -
155I ILE 3.5 5.6 - - - +
156I ALA* 3.7 31.4 - - + -
157I LEU* 4.9 1.1 - - - -
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Residues in contact with LEU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G LEU* 3.9 16.6 - - + -
59G TYR* 5.7 1.3 - - + -
119G TYR* 5.7 2.2 - - - +
57H LEU* 3.8 35.9 - - + -
123H VAL* 5.2 0.2 - - + -
157H LEU* 5.2 0.4 - - + -
56I TYR* 1.3 71.9 - - - +
58I ILE* 1.3 68.0 + - - +
59I TYR* 4.4 13.4 - - + -
121I GLY* 5.0 1.3 - - - -
122I GLY* 3.6 22.0 - - - +
123I VAL* 4.3 9.6 - - + +
153I GLY 4.0 0.2 - - - +
154I ILE* 3.0 25.5 - - - +
155I ILE* 2.9 34.2 + - + +
157I LEU* 3.9 17.5 - - + +
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Residues in contact with ILE 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I TYR* 4.2 11.0 - - + +
57I LEU* 1.3 77.9 - - - +
59I TYR* 1.3 64.8 + - - +
80I ILE* 3.7 31.2 - - + -
93I LEU* 4.0 16.8 - - + -
94I LEU* 4.0 3.7 - - + +
121I GLY* 3.1 3.6 - - - -
122I GLY 2.9 36.5 + - - +
124I PHE* 4.0 13.9 - - + -
126I LEU* 4.1 10.5 - - + -
132I LEU* 3.6 32.1 - - + -
152I PHE* 4.1 5.4 - - + -
153I GLY 3.6 3.8 - - - +
154I ILE* 3.9 20.9 - - + -
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Residues in contact with TYR 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H LEU* 5.6 2.2 - - + -
121H GLY 3.6 12.1 - - - -
122H GLY* 3.5 15.3 - - - -
123H VAL* 2.8 41.0 + - + +
14I ALA 4.1 0.7 + - - -
15I HIS* 2.6 36.1 + - - +
57I LEU* 4.4 18.4 - - + -
58I ILE* 1.3 80.5 - - - +
60I SER* 1.3 66.4 + - - +
80I ILE* 3.9 4.3 - - - -
119I TYR* 3.4 15.9 - - + +
120I LEU 3.1 13.9 - - - +
121I GLY* 4.0 2.7 - - - -
151I TYR* 3.7 14.4 - + - -
152I PHE* 3.3 3.8 - - - -
153I GLY* 2.9 57.5 + - - +
154I ILE* 4.0 3.6 - - - -
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Residues in contact with SER 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I TRP* 4.4 2.6 - - - -
59I TYR* 1.3 82.4 - - - +
61I GLN* 1.3 66.3 + - - +
78I HIS* 2.9 29.9 + - - -
80I ILE* 3.8 16.2 - - - -
119I TYR* 3.6 4.1 - - - -
120I LEU* 2.9 31.8 + - - +
134I ALA* 4.0 8.0 - - - +
151I TYR* 2.9 17.3 + - - -
152I PHE* 4.0 8.6 - - - +
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Residues in contact with GLN 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H SER 3.4 14.8 - - - +
96H ALA* 4.1 9.3 - - - +
118H ILE* 5.6 0.2 - - - +
119H TYR 3.3 24.7 + - - -
120H LEU* 3.4 14.5 - - - +
60I SER* 1.3 76.3 + - - +
62I VAL* 1.3 76.0 + - - +
63I LEU* 5.3 1.0 - - - +
78I HIS* 3.9 0.2 - - - -
117I PRO* 4.9 6.5 - - - +
118I ILE 3.3 17.2 - - - +
119I TYR* 4.0 7.4 - - + +
149I GLN 3.2 17.5 - - - +
150I VAL* 3.1 4.5 - - - +
151I TYR* 2.8 69.4 + - + +
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Residues in contact with VAL 62 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I LEU* 4.6 7.6 - - + -
28I TRP* 5.0 1.1 - - + -
60I SER* 4.5 1.6 - - - +
61I GLN* 1.3 80.6 - - - +
63I LEU* 1.3 61.3 + - - +
64I PHE* 3.4 33.2 - - + -
78I HIS* 3.4 40.8 - - + +
116I GLU 4.2 0.2 - - - +
117I PRO* 3.4 2.9 - - - +
118I ILE* 3.1 26.7 + - + +
136I ILE* 3.7 16.8 - - + -
142I LEU* 4.6 8.1 - - + -
149I GLN 3.8 2.9 - - - -
150I VAL* 4.2 13.5 - - + -
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Residues in contact with LEU 63 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H SER 5.4 0.2 - - - +
96H ALA* 4.8 3.6 - - + -
97H ILE* 4.3 22.2 - - + +
61I GLN* 5.3 0.4 - - - +
62I VAL* 1.3 74.0 - - - +
64I PHE* 1.3 78.2 + - - +
115I TYR* 4.3 12.1 - - + -
116I GLU 3.9 17.3 - - - +
117I PRO* 4.2 10.1 - - + -
142I LEU* 3.8 4.1 - - - +
143I LEU* 2.8 47.1 + - + +
149I GLN* 3.5 52.4 + - + +
150I VAL* 3.8 4.6 - - - +
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Residues in contact with PHE 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62I VAL* 3.4 22.9 - - + -
63I LEU* 1.3 82.2 - - - +
65I LYS* 1.3 59.9 + - - +
76I LEU* 3.5 56.1 - - + -
77I THR 4.1 9.9 - - - -
114I TRP* 3.8 7.4 - - + -
115I TYR* 3.4 1.9 - - - -
116I GLU 2.9 44.7 + - - +
118I ILE* 4.0 14.6 - - + -
136I ILE* 3.8 38.6 - - + -
137I ASN* 4.7 0.2 - - - -
138I ARG* 3.9 17.3 - - + -
141I TYR* 3.3 18.2 - - + +
142I LEU* 4.6 2.0 - - + -
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Residues in contact with LYS 65 (chain I).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64I PHE* 1.3 76.6 - - - +
66I GLY* 1.3 64.8 + - - +
67I GLN* 4.0 22.4 - - - +
113I PRO* 4.6 3.1 - - - -
114I TRP* 3.2 17.7 - - - +
115I TYR* 3.2 33.3 + - + -
140I ASP 5.0 0.2 - - - +
141I TYR* 2.7 32.9 + - - +
143I LEU* 3.5 44.6 - - + +
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Residues in contact with GLY 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LYS* 1.3 76.2 - - - +
67I GLN* 1.3 66.5 + - - +
113I PRO* 3.2 3.2 - - - +
114I TRP* 2.8 61.5 + - - -
141I TYR* 4.0 9.4 - - - -
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Residues in contact with GLN 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LYS* 4.0 16.1 - - + +
66I GLY* 1.3 70.1 - - - +
68I GLY* 1.3 69.0 + - - +
69I CYS 5.0 1.2 - - - -
70I PRO* 5.5 0.9 - - - +
111I ALA 4.7 0.4 - - - -
113I PRO* 3.0 35.4 - - - +
141I TYR* 5.3 1.2 - - - -
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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