Contacts of the strand formed by residues 94 - 103 (chain H) in PDB entry 1MWA
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 THR 94 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10H THR* 4.2 0.4 - - + -
11H ALA 3.3 3.6 - - - -
12H VAL* 3.2 26.3 - - + +
92H SER* 5.3 0.5 + - - -
93H HIS* 1.3 80.7 + - - +
95H ILE* 1.3 68.5 + - - +
96H GLN* 3.7 32.5 - - + +
118H TYR* 3.1 8.6 - - - -
119H ASP* 2.6 41.0 + - - -
31L HIS* 4.2 12.1 - - + -
32L PRO* 5.3 1.4 - - - +
33L PRO* 3.7 12.1 - - - +
62L PHE* 4.2 10.3 - - + -
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Residues in contact with ILE 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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9H VAL 3.5 0.5 - - - +
10H THR* 3.3 5.4 - - - -
11H ALA* 2.9 33.9 + - + +
74H PHE* 3.5 33.8 - - + -
77H SER* 3.9 13.0 - - - -
78H LEU* 3.8 42.4 - - + +
81H LEU* 3.8 27.4 - - + -
94H THR* 1.3 77.4 - - - +
96H GLN* 1.3 69.3 + - - +
116H TYR* 4.1 19.1 - - + -
117H ALA 3.3 8.3 - - - +
118H TYR* 4.1 1.6 - - + -
8P VAL* 6.3 0.2 - - + -
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Residues in contact with GLN 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL 3.0 6.1 - - - +
10H THR* 4.2 6.1 - - + -
94H THR* 3.7 9.4 - - + +
95H ILE* 1.3 81.9 - - - +
97H VAL* 1.3 62.3 + - - +
116H TYR* 3.4 3.1 - - - +
117H ALA* 2.8 36.5 + - + +
120H GLY* 3.8 7.6 + - - -
31L HIS* 2.5 30.6 + - - -
56L PHE* 3.5 23.8 - - + -
60L TRP* 2.8 49.0 + - + +
62L PHE* 3.3 21.2 - - + -
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Residues in contact with VAL 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H TYR 3.6 2.1 - - - +
8H PHE* 3.6 1.6 - - - -
9H VAL* 2.8 59.6 + - + +
74H PHE* 3.5 28.3 - - + -
96H GLN* 1.3 78.0 - - - +
98H ILE* 1.3 75.5 + - - +
99H SER* 4.3 1.6 - - - -
114H GLN* 4.2 4.9 - - + -
115H GLN 3.0 13.0 - - - +
116H TYR* 4.0 21.3 - - + -
56L PHE* 4.0 0.5 - - - -
60L TRP* 4.3 0.4 - - - -
5P PHE* 3.9 23.3 - - + -
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Residues in contact with ILE 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG* 4.9 2.9 - - + -
7H TYR 3.5 3.4 - - - -
8H PHE* 3.9 35.4 - - + -
97H VAL* 1.3 75.7 - - - +
99H SER* 1.3 63.9 + - - +
113H TYR* 3.6 24.5 - - + +
114H GLN* 3.2 2.8 + - - -
115H GLN* 2.8 48.3 + - - +
56L PHE* 3.7 23.8 - - + -
58L LYS* 4.1 23.1 - - + +
60L TRP* 3.7 22.0 - - + -
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Residues in contact with SER 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG* 3.3 1.9 - - - -
7H TYR* 2.8 40.9 + - - +
97H VAL* 4.3 6.7 - - - -
98H ILE* 1.3 77.0 - - - +
100H GLY* 1.3 59.5 + - - +
113H TYR* 3.1 9.6 - - - -
114H GLN* 3.2 29.4 + - - -
159H TYR* 4.1 17.2 + - - -
160H LEU* 5.1 1.1 - - - +
2P GLN* 4.5 5.6 + - - -
3P TYR* 4.8 0.2 - - - +
5P PHE* 4.3 11.5 - - - -
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Residues in contact with GLY 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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5H LEU 3.0 13.0 - - - -
6H ARG* 4.0 0.7 - - - -
7H TYR* 5.9 0.2 - - - -
99H SER* 1.3 77.6 + - - +
101H CYS* 1.3 61.2 + - - -
112H GLY* 3.4 2.6 - - - -
113H TYR* 2.9 45.8 + - - -
159H TYR* 5.3 2.0 - - - -
160H LEU* 3.6 9.6 - - - +
164H CYS* 3.9 9.6 - - - -
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Residues in contact with CYS 101 (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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3H HIS 3.9 0.3 - - - +
4H SER* 3.0 3.8 - - - -
5H LEU* 2.8 42.0 + - - -
100H GLY* 1.3 73.9 - - - +
102H GLU* 1.3 65.1 + - - +
103H VAL* 4.1 5.1 + - - -
109H LEU* 3.5 22.4 - - + -
111H ARG 3.2 4.9 - - - +
112H GLY* 4.9 1.1 - - - -
113H TYR* 3.8 1.7 + - - -
160H LEU 3.9 4.3 - - - +
164H CYS* 2.1 59.9 - - + -
165H VAL* 3.7 7.0 - - - -
168H LEU* 4.5 1.8 - - - +
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Residues in contact with GLU 102 (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 PRO* 6.0 2.2 - - + -
3H HIS 3.3 8.1 - - - +
4H SER* 4.0 4.5 - - - -
6H ARG* 2.5 33.0 + - - +
101H CYS* 1.3 74.7 - - - +
103H VAL* 1.3 55.0 + - - +
109H LEU* 3.6 1.6 - - - -
110H LEU* 2.6 40.8 + - + +
111H ARG* 2.7 64.5 + - + +
113H TYR* 3.4 15.5 - - + -
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Residues in contact with VAL 103 (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 PRO* 3.4 2.1 - - - +
3H HIS* 2.8 32.8 + - + +
101H CYS* 4.6 3.4 - - - +
102H GLU* 1.3 80.1 - - - +
104H GLY* 1.3 74.7 + - - +
107H GLY* 3.7 18.8 - - - +
108H ARG 3.1 17.5 - - - +
109H LEU* 4.2 1.8 - - - -
110H LEU* 3.9 3.8 - - - -
165H VAL* 4.1 30.5 - - + +
168H LEU* 3.4 29.4 - - + -
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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