Contacts of the strand formed by residues 33 - 40 (chain H) in PDB entry 1YEE
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 TRP 33 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H TYR* 1.3 77.7 - - - +
34H ILE* 1.3 59.9 + - - +
35H HIS* 3.9 21.6 - - + +
50H ARG* 3.6 30.1 - - + -
51H ILE* 3.2 26.2 - - - -
52H TYR* 3.3 30.8 - + + -
56H SER* 3.1 33.4 - - - -
58H TYR* 3.5 38.1 - + - -
93H VAL 4.0 6.4 - - - +
94H ARG* 4.0 15.2 - - - +
95H TRP 4.3 1.7 + - - -
96H GLY 5.3 1.7 + - - -
97H PHE 4.8 6.2 + - - +
99H PRO* 3.8 34.0 - - + +
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Residues in contact with ILE 34 (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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4H LEU* 4.5 9.2 - - + -
22H CYS* 4.7 0.7 - - - -
24H THR* 4.1 16.4 - - + -
27H TYR* 3.4 25.4 - - - +
29H PHE* 4.6 2.9 - - + -
32H TYR 4.2 7.6 - - - +
33H TRP* 1.3 79.0 - - - +
35H HIS* 1.3 69.6 + - - +
36H TRP* 4.1 17.6 - - - +
50H ARG* 3.1 3.5 - - - +
51H ILE* 2.9 41.4 + - + +
52H PRO* 4.3 14.8 - - + -
78H ALA* 4.2 15.3 - - + -
92H CYS* 4.2 13.0 - - + -
93H VAL 3.4 9.2 - - - +
94H ARG* 4.6 4.0 - - + -
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Residues in contact with HIS 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H TRP* 3.9 22.7 - - - +
34H ILE* 1.3 80.3 - - - +
36H TRP* 1.3 65.1 + - - +
47H TRP* 3.0 26.0 + - + +
49H ALA 3.3 4.7 - - - -
50H ARG* 3.5 27.5 - - + +
91H PHE 3.6 0.3 - - - +
92H CYS* 3.3 5.4 - - - -
93H VAL* 2.8 36.1 + - + +
95H TRP* 3.6 26.9 - + + +
97H PHE* 6.1 1.2 - - - +
551H PNB 3.5 41.2 - + - +
96L TYR* 4.3 3.8 - + - -
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Residues in contact with TRP 36 (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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6H GLU* 4.0 17.0 - - - -
20H LEU* 3.9 31.6 - - + -
21H SER 4.3 2.2 - - - -
22H CYS* 3.8 25.4 - - + -
34H ILE* 4.1 12.9 - - + +
35H HIS* 1.3 78.8 - - - +
37H VAL* 1.3 63.0 - - - +
47H TRP* 4.1 2.4 - - - -
48H ILE* 3.0 31.7 + - + +
49H ALA 2.8 12.4 + - - +
51H ILE* 5.3 1.6 - - - +
69H LEU* 3.7 31.5 - - + +
78H ALA* 4.2 7.4 - - + +
79H TYR* 4.0 8.3 + - - -
80H MET* 3.6 57.6 - - + +
90H TYR* 4.5 4.9 - - + -
91H PHE 3.2 17.9 - - - -
92H CYS* 3.9 13.0 - - + -
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Residues in contact with VAL 37 (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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36H TRP* 1.3 79.9 - - - +
38H LYS* 1.3 65.4 + - - +
45H LEU* 3.8 31.2 - - + -
46H GLU 3.4 15.0 - - - +
47H TRP* 4.4 10.3 - - + -
48H ILE* 4.1 3.6 - - - -
89H VAL 3.9 0.3 - - - +
90H TYR* 3.3 3.8 - - - +
91H PHE* 2.7 44.7 + - + +
93H VAL* 4.2 8.3 - - + -
103H TRP* 4.3 16.4 - - + -
551H PNB 3.9 31.2 - - - +
98L PHE* 4.7 4.9 - - + -
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Residues in contact with LYS 38 (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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37H VAL* 1.3 75.7 - - - +
39H GLN* 1.3 65.8 + - - +
40H ARG* 4.2 17.8 + - + +
44H GLY 3.5 0.7 - - - +
45H LEU* 3.4 5.7 - - - -
46H GLU* 2.8 56.0 + - + +
48H ILE* 3.7 17.9 - - + +
63H PHE* 4.5 19.0 - - + -
85H ASP 3.6 19.7 + - - -
86H ASP* 4.4 6.7 + - - +
88H ALA* 3.8 19.7 - - + -
89H VAL 3.7 2.5 - - - -
90H TYR* 3.7 32.0 + - + -
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Residues in contact with GLN 39 (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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38H LYS* 1.3 77.3 - - - +
40H ARG* 1.3 67.1 + - - +
41H ALA* 4.0 1.5 + - - -
43H ALA* 4.6 6.2 - - - +
44H GLY 3.3 12.6 + - - +
45H LEU* 3.8 19.8 - - + +
88H ALA* 3.3 3.2 - - - +
89H VAL* 2.8 44.6 + - + +
91H PHE* 3.9 15.3 - - + -
38L GLN* 2.7 44.3 + - - +
85L LEU* 6.0 0.2 - - - +
87L TYR* 3.8 14.1 + - - -
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Residues in contact with ARG 40 (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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38H LYS* 4.2 16.6 - - + +
39H GLN* 1.3 77.0 - - - +
41H ALA* 1.3 57.1 + - - +
42H ALA* 2.4 33.6 + - + +
43H ALA 3.7 1.9 + - - -
44H GLY* 3.6 10.4 + - - +
84H SER 4.0 4.9 + - - -
85H ASP* 3.3 52.5 + - - +
87H SER* 3.2 27.9 + - - +
88H ALA* 4.0 6.3 - - + +
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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
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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