Contacts of the strand formed by residues 88 - 95 (chain H) in PDB entry 3GBN
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 ALA 88 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H ARG* 4.1 11.9 - - - +
39H GLN 3.5 21.3 - - - +
40H ALA* 3.8 5.6 - - + +
41H PRO* 4.7 3.4 - - - -
86H ASP 3.2 4.5 + - - +
87H THR* 1.3 79.8 - - - +
89H MET* 1.3 62.4 + - - +
90H TYR* 3.4 24.1 - - + -
108H THR* 3.5 5.3 - - - +
109H VAL 2.9 32.2 + - - +
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Residues in contact with MET 89 (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 ARG* 3.2 5.4 - - - +
39H GLN* 2.9 44.1 + - + +
41H PRO* 5.7 0.2 - - - +
88H ALA* 1.3 73.2 - - - +
90H TYR* 1.3 61.0 + - - +
91H TYR* 3.6 35.0 + - + +
105H LYS 4.5 4.3 - - - +
106H GLY* 3.6 29.8 - - - +
107H THR* 3.6 4.5 - - - -
108H THR* 3.6 22.0 - - - +
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Residues in contact with TYR 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLU* 2.7 24.2 - - - +
18H VAL* 6.0 1.3 - - + -
20H VAL* 5.1 1.6 - - + -
36H TRP* 4.7 11.4 - + + -
37H VAL 3.8 2.0 - - - -
38H ARG* 3.1 36.4 + - + -
48H MET* 3.6 29.8 - - + -
80H MET* 3.6 24.2 - - + -
82H LEU* 3.7 8.0 - - + +
86H ASP* 2.6 36.2 + - - +
88H ALA* 3.4 21.1 - - + -
89H MET* 1.3 71.6 - - - +
91H TYR* 1.3 56.7 + - - +
107H THR* 2.7 37.9 + - + +
109H VAL* 3.6 29.1 - - + +
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Residues in contact with TYR 91 (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* 3.5 2.5 - - - -
36H TRP* 3.3 9.0 - - - -
37H VAL* 2.7 47.4 + - + +
38H ARG* 4.8 0.7 - - - -
39H GLN* 3.9 26.5 + - + -
45H PRO* 6.2 0.2 - - + -
89H MET* 3.6 29.8 - - + +
90H TYR* 1.3 73.9 - - - +
92H CYS* 1.3 61.4 + - - +
103H TRP* 3.8 29.2 - + + -
104H GLY 3.5 13.0 - - - -
105H LYS 3.6 19.3 + - - -
106H GLY* 3.5 13.5 - - - -
38L GLN* 3.5 17.5 + - - -
41L GLY 5.9 0.3 - - - -
42L THR 3.7 7.8 + - - -
43L ALA* 3.6 18.6 - - + -
44L PRO* 4.0 10.8 - - + -
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Residues in contact with CYS 92 (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* 3.9 12.1 - - - -
6H GLU* 3.2 26.0 + - - -
22H CYS* 2.2 52.7 - - + -
34H ILE* 4.2 6.5 - - + -
35H SER 3.3 9.4 - - - +
36H TRP* 3.9 10.2 - - + -
91H TYR* 1.3 76.4 - - - +
93H ALA* 1.3 63.2 - - - +
103H TRP* 3.6 0.9 - - - -
104H GLY 2.9 25.1 + - - -
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Residues in contact with ALA 93 (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* 4.0 3.1 - - - -
34H ILE* 3.5 3.3 - - - -
35H SER* 2.9 34.8 + - - +
37H VAL* 5.1 2.0 - - + -
91H TYR 4.2 0.2 + - - -
92H CYS* 1.3 78.1 - - - +
94H LYS* 1.3 62.1 + - - +
95H HIS* 4.3 0.5 - - - -
100H MET* 3.8 25.0 + - + -
102H VAL 3.3 12.8 - - - +
103H TRP* 3.7 26.9 - - + -
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Residues in contact with LYS 94 (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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1H GLU* 5.2 2.6 + - - +
2H VAL* 4.1 22.0 - - + -
4H LEU* 3.8 7.2 - - + +
32H TYR* 3.6 50.6 - - + +
33H ALA 3.5 4.7 - - - +
34H ILE* 4.1 5.8 - - + -
93H ALA* 1.3 74.8 - - - +
95H HIS* 1.3 74.0 + - - +
96H MET* 4.4 3.8 + - - +
100H MET* 3.1 6.7 - - - +
101H ASP* 2.8 62.7 + - - +
102H VAL* 2.9 34.4 + - + +
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Residues in contact with HIS 95 (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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32H TYR* 3.4 6.6 - - - +
33H ALA* 2.9 32.3 + - + +
34H ILE 3.9 1.6 - - - -
35H SER* 2.7 35.8 + - - -
47H TRP* 4.9 0.7 - - - -
94H LYS* 1.3 95.7 + - - +
96H MET* 1.3 63.8 + - - +
97H GLY 3.3 17.0 - - - +
99H GLN 3.8 11.2 - - - +
100H THR* 3.0 81.2 + - + +
101H ASP* 3.7 3.1 - - - -
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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