Contacts of the strand formed by residues 91 - 100 (chain H) in PDB entry 1I9J
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 91 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 4.3 7.2 - - + -
39H GLN 3.0 28.9 - - - +
40H THR* 3.9 9.4 - - + +
41H ALA 5.5 0.4 - - - +
89H ASP 3.2 8.0 + - - +
90H THR* 1.3 81.0 - - - +
92H MET* 1.3 63.7 + - - +
93H TYR* 3.2 13.7 - - + -
113H LEU* 4.6 6.7 - - - +
114H VAL 2.9 32.1 + - - -
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Residues in contact with MET 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H VAL 3.9 0.2 - - - +
38H ARG* 3.1 6.1 - - - +
39H GLN* 2.9 38.0 + - + +
91H ALA* 1.3 75.1 - - - +
93H TYR* 1.3 61.0 + - - +
94H TYR* 3.6 35.9 + - + +
110H GLN 4.6 2.2 - - - +
111H GLY* 3.5 23.1 - - - +
112H THR 3.9 0.7 - - - -
113H LEU* 3.5 44.3 - - + +
154H PRO* 6.1 2.2 - - + -
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Residues in contact with TYR 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLU* 3.7 7.8 - - - +
20H LEU* 3.8 17.5 - - + -
36H TRP* 4.2 7.6 - + + -
37H VAL 3.7 2.5 - - - -
38H ARG* 3.1 40.3 + - + -
48H VAL* 4.4 6.7 - - + -
67H PHE* 4.1 19.8 - + - -
80H LEU* 4.0 20.6 - - + -
82H MET* 4.2 7.9 - - - -
89H ASP* 2.6 32.6 + - - +
91H ALA* 3.2 24.7 - - + -
92H MET* 1.3 73.6 - - - +
94H TYR* 1.3 61.4 - - - +
111H GLY* 3.2 3.8 - - - -
112H THR* 3.0 35.6 + - + +
114H VAL* 3.8 23.1 - - + +
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Residues in contact with TYR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H GLU* 3.2 4.0 - - - +
36H TRP* 3.2 8.5 - - - -
37H VAL* 2.7 47.5 + - + +
38H ARG 5.2 0.2 - - - -
39H GLN* 3.9 20.2 + - + -
45H LEU* 5.3 1.3 - - + -
92H MET* 3.6 31.6 - - + +
93H TYR* 1.3 75.7 - - - +
95H CYS* 1.3 61.6 + - - +
96H ALA 4.2 0.2 + - - -
108H TRP* 3.6 34.3 - + + -
109H GLY 3.5 16.2 - - - -
110H GLN 3.6 15.2 + - - -
111H GLY* 3.9 6.3 - - - -
43L GLN* 3.6 17.0 + - - -
47L GLN 4.0 6.4 + - - -
48L SER* 3.5 23.5 - - - -
49L PRO* 4.2 10.5 - - + -
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Residues in contact with CYS 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 3.6 12.5 - - + +
5H VAL 4.7 0.9 - - - -
6H GLU* 2.7 28.1 + - - -
22H CYS* 2.0 54.1 - - + -
35H SER 3.2 11.2 - - - +
36H TRP* 3.9 11.0 - - + -
78H LEU* 4.2 5.6 - - + -
94H TYR* 1.3 74.4 - - - +
96H ALA* 1.3 62.0 + - - +
108H TRP* 3.6 1.9 - - - +
109H GLY 3.2 23.7 + - - -
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Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 3.7 5.4 - - - -
33H ALA 4.0 0.3 - - - +
34H LEU* 3.4 8.1 - - - +
35H SER* 2.9 34.7 + - - +
37H VAL* 5.5 3.6 - - + -
78H LEU* 5.3 0.3 - - - +
94H TYR 5.5 0.2 - - - +
95H CYS* 1.3 76.3 - - - +
97H ARG* 1.3 61.1 + - - +
105H LEU* 4.0 28.0 - - + -
107H TYR 3.0 17.3 - - - +
108H TRP* 4.3 17.7 - - + -
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Residues in contact with ARG 97 (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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2H VAL* 4.1 9.1 - - + +
4H LEU* 3.8 9.1 - - + +
27H PHE* 3.4 49.8 - - + +
32H TYR* 3.3 47.7 + - + -
33H ALA 3.7 1.6 - - - -
34H LEU* 3.5 23.6 - - + -
96H ALA* 1.3 74.6 - - - +
98H GLU* 1.3 85.1 + - - +
99H TYR* 3.3 11.1 + - - +
105H LEU* 3.7 2.3 - - - -
106H ALA 3.0 23.6 + - - -
107H TYR* 3.0 44.4 + - + -
1010H TES 4.6 2.2 - - - -
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Residues in contact with GLU 98 (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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31H THR 4.7 1.2 - - - +
32H TYR* 3.5 13.7 - - + -
33H ALA* 2.7 49.4 + - + +
53H SER* 5.6 0.9 + - - -
97H ARG* 1.3 100.2 + - - +
99H TYR* 1.3 63.0 + - - +
100H TYR* 3.9 4.7 - - - +
101H GLY* 3.5 11.1 + - - -
102H TYR* 2.5 41.6 + - - -
103H VAL 4.3 0.7 - - - +
104H GLY 3.2 11.4 - - - +
106H ALA* 4.3 1.0 - - - +
1010H TES 3.4 19.4 + - - +
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Residues in contact with TYR 99 (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* 3.5 7.8 - - - -
97H ARG* 3.3 16.8 + - - +
98H GLU* 1.3 75.7 - - - +
100H TYR* 1.3 91.3 + + + +
103H VAL* 3.0 21.4 + - + +
104H GLY 3.4 2.1 + - - -
106H ALA* 3.9 15.1 - - + +
107H TYR* 5.2 6.3 - - - -
51L LEU* 4.7 3.1 - - + -
54L TYR* 3.7 32.4 + + - -
60L PHE* 3.7 38.0 - + - -
61L SER* 5.0 9.6 + - - -
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Residues in contact with TYR 100 (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* 4.9 6.5 - - + -
98H GLU* 3.5 8.7 - - - -
99H TYR* 1.3 120.8 - + + +
101H GLY* 1.3 60.7 + - - +
102H TYR 3.2 2.5 - - - -
103H VAL* 2.7 52.2 + - + +
54L TYR* 4.0 20.6 + + - -
55L LYS* 4.2 16.9 + - - +
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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