Contacts of the strand formed by residues 54 - 67 (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 GLY 54 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H SER 3.6 0.4 + - - -
53H GLU* 1.3 76.6 - - - +
55H LEU* 1.3 60.7 + - - -
56H TYR* 3.3 13.7 - - - -
125H GLN* 3.5 17.5 + - - +
126H LEU 2.8 37.2 + - - -
156H ALA* 6.5 0.2 - - - -
7I THR 5.3 2.6 + - - -
8I PRO 4.2 4.3 - - - -
9I SER* 5.8 0.9 - - - -
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H GLY* 1.3 71.8 - - - -
56H TYR* 1.3 64.1 + - - +
123H VAL* 4.1 16.4 - - + -
124H PHE 3.4 1.1 - - - +
125H GLN* 3.3 38.4 - - + +
156H ALA* 3.7 2.3 - - - +
157H LEU* 3.0 41.7 + - + +
8I PRO* 3.6 13.1 + - + +
9I SER* 3.2 27.3 - - - +
13I VAL* 3.6 29.4 - - + -
36I LEU* 3.9 16.6 - - + -
155I ILE* 4.0 9.0 - - + -
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H PRO* 3.7 16.5 - - + +
50H VAL* 3.0 25.8 - - + +
51H PRO* 3.8 2.7 - - + +
52H SER* 3.0 42.0 + - - -
53H GLU 4.6 0.4 - - - -
54H GLY* 3.3 25.6 - - - -
55H LEU* 1.3 77.1 - - - +
57H LEU* 1.3 63.0 + - - +
58H ILE* 3.6 9.6 + - + +
122H GLY 3.6 0.9 - - - +
123H VAL* 3.2 7.1 - - - +
124H PHE 2.8 38.1 + - - +
126H LEU* 3.8 26.0 - - + -
154H ILE* 4.0 21.1 - - + -
155H ILE 3.5 7.2 - - - -
156H ALA* 3.7 30.5 - - + +
157H LEU* 4.5 0.9 - - - +
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Residues in contact with LEU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 4.0 23.1 - - + -
157G LEU* 5.3 0.7 - - + -
56H TYR* 1.3 72.3 - - - +
58H ILE* 1.3 67.6 + - - +
59H TYR* 4.4 13.3 - - + -
121H GLY* 4.9 1.6 - - - -
122H GLY* 3.6 20.9 - - - +
123H VAL* 4.3 9.2 - - + +
154H ILE* 3.0 26.0 - - - +
155H ILE* 2.9 34.2 + - + +
157H LEU* 3.8 18.2 - - + +
57I LEU* 3.8 27.6 - - + -
59I TYR* 5.6 2.0 - - + -
119I TYR* 5.7 2.2 - - - +
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Residues in contact with ILE 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H TYR* 4.1 12.3 - - + +
57H LEU* 1.3 77.9 - - - +
59H TYR* 1.3 65.9 + - - +
80H ILE* 3.7 30.7 - - + -
93H LEU* 3.9 17.7 - - + -
94H LEU* 4.0 3.6 - - + +
121H GLY* 3.1 3.6 - - - -
122H GLY 2.9 34.4 + - - +
124H PHE* 4.0 12.8 - - + -
126H LEU* 4.1 9.9 - - + -
132H LEU* 3.6 32.1 - - + -
152H PHE* 4.1 4.9 - - + -
153H GLY 3.6 3.6 - - - +
154H ILE* 3.9 20.9 - - + -
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Residues in contact with TYR 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 5.7 1.6 - - + -
121G GLY 3.7 12.8 - - - -
122G GLY* 3.5 14.1 - - - -
123G VAL* 2.8 40.9 + - + +
14H ALA 4.2 0.9 + - - -
15H HIS* 2.6 36.3 + - - +
57H LEU* 4.4 18.4 - - + -
58H ILE* 1.3 80.5 - - - +
60H SER* 1.3 66.8 + - - +
80H ILE* 4.0 4.7 - - - -
119H TYR* 3.5 15.9 - - - +
120H LEU 3.0 13.7 - - - +
121H GLY* 4.0 2.7 - - - -
151H TYR* 3.7 15.0 - + - -
152H PHE* 3.3 3.5 - - - -
153H GLY* 2.9 58.5 + - - +
154H ILE* 4.0 4.7 - - - -
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Residues in contact with SER 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H TRP* 4.4 2.8 - - - -
59H TYR* 1.3 81.1 - - - +
61H GLN* 1.3 65.6 + - - +
78H HIS* 2.9 30.7 + - - -
80H ILE* 3.8 16.6 - - - -
119H TYR* 3.6 4.2 - - - -
120H LEU* 2.9 33.1 + - - +
134H ALA* 4.0 7.3 - - - +
151H TYR* 2.9 16.6 + - - -
152H PHE* 3.9 9.3 - - - +
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Residues in contact with GLN 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G SER 3.3 16.9 - - - +
96G ALA* 4.1 9.1 - - - +
119G TYR 3.3 11.1 + - - -
120G LEU* 3.2 28.7 - - - +
60H SER* 1.3 76.5 + - - +
62H VAL* 1.3 75.2 + - - +
63H LEU* 5.3 0.3 - - - +
78H HIS* 3.9 0.4 - - - -
117H PRO* 4.9 5.2 - - - +
118H ILE 3.3 17.7 - - - +
119H TYR* 4.0 7.3 - - + +
149H GLN 3.1 18.4 - - - +
150H VAL* 3.1 4.9 - - - +
151H TYR* 2.8 65.9 + - + +
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Residues in contact with VAL 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H LEU* 4.6 7.9 - - + -
28H TRP* 5.0 1.6 - - + -
60H SER* 4.5 1.3 - - - +
61H GLN* 1.3 81.6 - - - +
63H LEU* 1.3 60.3 + - - +
64H PHE* 3.4 33.4 - - + -
78H HIS* 3.4 40.2 - - + +
116H GLU 4.2 0.2 - - - +
117H PRO* 3.4 2.1 - - - +
118H ILE* 3.0 31.9 + - + -
136H ILE* 3.7 17.0 - - + -
142H LEU* 4.6 8.7 - - + -
149H GLN 3.8 4.7 - - - -
150H VAL* 4.2 13.0 - - + -
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Residues in contact with LEU 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ALA* 4.6 3.8 - - - -
97G ILE* 4.2 30.3 - - + +
61H GLN* 5.3 0.9 - - - +
62H VAL* 1.3 75.2 - - - +
64H PHE* 1.3 78.7 + - - +
115H TYR* 4.3 7.2 - - + -
116H GLU 3.8 17.5 - - - +
117H PRO* 4.2 8.1 - - + -
142H LEU* 3.8 5.0 - - - +
143H LEU* 2.8 46.8 + - + +
149H GLN* 3.5 53.3 + - + +
150H VAL* 3.8 4.4 - - - +
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Residues in contact with PHE 64 (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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62H VAL* 3.4 22.2 - - + -
63H LEU* 1.3 81.0 - - - +
65H LYS* 1.3 59.8 + - - +
76H LEU* 3.5 56.1 - - + -
77H THR 4.1 8.7 - - - -
114H TRP* 3.8 7.0 - - + -
115H TYR* 3.4 1.9 - - - -
116H GLU 2.9 43.3 + - - +
118H ILE* 3.9 15.7 - - + -
136H ILE* 3.8 38.4 - - + -
137H ASN* 4.7 0.4 - - - -
138H ARG* 3.9 17.3 - - + -
141H TYR* 3.3 18.8 - - + +
142H LEU* 4.5 2.0 - - + -
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Residues in contact with LYS 65 (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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64H PHE* 1.3 76.6 - - - +
66H GLY* 1.3 65.8 + - - +
67H GLN* 4.0 23.1 - - + +
113H PRO* 4.6 3.4 - - - -
114H TRP* 3.2 16.6 - - - +
115H TYR* 3.1 32.0 + - + -
140H ASP 5.0 0.2 - - - +
141H TYR* 2.7 31.9 + - - +
143H LEU* 3.5 43.9 - - + +
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Residues in contact with GLY 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H LYS* 1.3 77.2 - - - +
67H GLN* 1.3 67.2 + - - -
113H PRO* 3.2 2.3 - - - +
114H TRP* 2.8 61.7 + - - -
141H TYR* 4.0 9.2 - - - -
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Residues in contact with GLN 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H LYS* 4.0 15.7 - - - +
66H GLY* 1.3 70.8 - - - +
68H GLY* 1.3 69.0 + - - +
69H CYS 5.0 1.2 - - - -
70H PRO* 5.5 0.7 - - - +
111H ALA 5.3 0.7 - - - +
112H LYS 5.1 0.2 - - - -
113H PRO* 3.0 28.0 - - - +
141H TYR* 5.4 1.0 - - - -
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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
------------------------------------------------------------
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