Contacts of the strand formed by residues 99 - 105 (chain A) in PDB entry 1MAQ
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 ARG 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLU* 3.0 29.3 + - - -
94A ALA* 3.2 18.4 + - - +
97A SER* 2.8 31.8 - - - +
98A GLY* 1.4 73.2 - - - +
100A TYR* 1.3 58.1 + - - +
244A ILE* 4.7 12.5 + - - +
249A ASP* 2.7 32.1 + - - -
273A ILE* 3.0 24.6 - - + +
274A CYS* 2.8 47.7 + - - +
275A ARG* 4.1 17.1 + - - +
276A ASP* 3.8 15.9 - - - -
280A ALA* 4.4 0.4 - - - -
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A THR* 5.0 3.4 - - + -
81A ARG* 4.0 15.7 - - - +
84A ALA* 3.3 18.4 - - + -
88A LEU* 4.5 5.2 - - + -
94A ALA 3.7 15.9 - - - +
95A PHE* 3.2 54.2 - + - -
98A GLY* 3.0 16.2 + - - +
99A ARG* 1.3 80.8 - - - +
101A VAL* 1.3 65.5 + - - +
102A THR* 3.4 24.9 - - - -
271A THR* 4.4 3.4 - - + -
272A VAL 3.4 6.3 - - - +
273A ILE* 3.7 23.3 - - + -
274A CYS* 5.0 0.2 - - - -
280A ALA* 3.6 12.6 - - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR* 1.3 78.7 - - - +
102A THR* 1.3 73.3 + - - +
103A VAL* 4.5 7.0 - - + -
270A PHE 3.7 1.2 - - - +
271A THR* 3.0 4.5 - - - +
272A VAL* 2.9 38.5 + - + +
274A CYS* 4.4 2.0 - - - -
280A ALA* 3.7 25.1 - - + +
283A VAL* 4.1 24.2 - - + -
284A GLU* 3.7 36.8 - - + +
287A LEU* 4.6 5.4 - - + +
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA* 4.6 2.9 - - - +
80A THR* 3.4 46.2 + - - +
83A SER* 4.5 5.2 - - - -
84A ALA* 3.4 8.6 - - - +
100A TYR* 3.4 23.9 - - - -
101A VAL* 1.3 78.4 - - - +
103A VAL* 1.3 69.2 + - - +
269A ALA* 3.7 23.3 - - + -
270A PHE 3.4 3.6 - - - +
271A THR* 3.0 22.7 + - - +
284A GLU* 4.9 1.4 - - - +
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Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA* 3.5 26.0 - - + +
80A THR* 3.9 2.2 - - - -
101A VAL* 4.5 1.8 - - + -
102A THR* 1.3 79.5 - - - +
104A GLN* 1.3 77.0 + - - +
105A GLY* 5.2 1.1 - - - -
114A VAL* 5.0 6.3 - - + -
269A ALA* 3.3 3.9 - - - -
270A PHE* 2.9 42.8 + - + +
284A GLU* 4.4 9.0 - - - +
287A LEU* 4.3 24.5 - - + -
288A LYS* 5.6 1.8 - - + +
291A ILE* 3.5 27.8 - - + -
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LEU* 3.9 3.0 - - - +
73A ILE 5.1 1.2 - - - +
74A ALA 2.7 21.0 + - - +
75A GLY* 3.0 6.2 - - - -
76A LEU* 2.7 32.4 + - - +
79A PHE* 3.8 23.3 - - + -
80A THR* 3.7 3.4 + - - +
103A VAL* 1.3 83.2 - - - +
105A GLY* 1.3 64.5 + - - +
266A ARG 5.5 2.2 + - - -
267A ALA* 5.9 2.5 - - - +
268A GLY 3.7 6.7 - - - +
291A ILE* 5.0 0.5 - - - +
295A TYR* 3.7 11.1 + - - -
298A PRO* 3.6 26.4 - - + +
299A PRO* 2.9 29.9 + - - +
303A ALA* 3.2 25.0 - - - +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A VAL* 3.4 4.2 + - - -
104A GLN* 1.3 79.8 - - - +
106A ILE* 1.3 55.5 + - - -
107A SER 2.7 18.8 + - - -
110A GLY 4.9 0.7 - - - -
111A SER* 3.4 22.4 - - - -
114A VAL* 5.9 1.6 - - - -
266A ARG 4.0 4.3 - - - +
267A ALA* 4.3 0.3 - - - -
268A GLY 2.8 25.2 + - - +
270A PHE* 5.2 0.4 - - - -
295A TYR* 4.2 6.5 - - - -
298A PRO* 5.5 2.4 - - - +
299A PRO* 5.6 0.7 - - - +
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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