Contacts of the strand formed by residues 99 - 105 (chain B) in PDB entry 2MPR
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 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B GLN* 3.8 24.7 - - + +
88B GLY 3.4 12.8 - - - +
89B LYS* 3.6 21.6 - - + +
97B GLY 4.2 4.7 + - - -
98B SER* 1.3 74.7 - - - +
100B ILE* 1.3 74.0 + - - +
101B TRP* 4.2 1.2 - - + -
128B GLY 4.0 0.2 - - - +
129B ILE* 3.2 3.9 - - - -
130B GLU* 2.9 56.2 + - + +
131B ASN* 4.9 6.1 + - - -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLN* 3.5 0.9 - - - -
88B GLY 2.9 37.0 + - - +
91B LEU* 4.1 13.5 - - + -
92B ILE* 4.0 21.5 - - + -
98B SER* 5.3 0.7 - - - +
99B THR* 1.3 75.7 - - - +
101B TRP* 1.3 62.8 + - - +
128B GLY 3.5 6.3 - - - +
129B ILE* 4.0 26.2 - - + -
361C TRP* 4.0 41.3 - - + -
373C ILE* 3.8 21.3 - - + +
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Residues in contact with TRP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASN* 4.8 1.3 - - + +
86B VAL 3.2 16.2 - - - +
87B GLN* 3.8 15.5 - - + -
99B THR* 4.2 6.5 - - + -
100B ILE* 1.3 77.8 - - - +
102B ALA* 1.3 70.2 + - - +
103B GLY 3.6 20.4 - - - -
105B ARG* 3.1 42.7 - - + +
107B TYR* 3.5 36.3 - + + -
124B GLY 5.2 1.3 - - - -
126B GLY* 3.6 12.6 - - - -
127B ALA* 3.2 25.3 - - - +
128B GLY* 3.1 51.2 + - - +
129B ILE 4.2 0.8 - - - +
130B GLU* 4.1 9.3 + - + +
141B LEU 5.1 0.2 + - - -
142B ALA* 4.1 7.6 - - + -
144B THR* 4.4 11.4 - - + -
373C ILE* 4.3 6.6 - - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASN* 3.3 4.2 - - - +
86B VAL 3.2 26.3 + - - -
101B TRP* 1.3 78.8 - - - +
103B GLY* 1.3 58.9 + - - +
126B GLY 3.5 11.0 - - - +
127B ALA* 4.2 7.4 - - + -
10C GLY* 5.3 0.2 - - - -
373C ILE* 4.3 13.1 - - + +
421C ALA* 4.4 3.1 - - + +
422C GLN* 4.0 35.2 - - - +
423C MET* 3.4 9.9 - - + +
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA 3.4 11.0 - - - -
85B ASN* 3.8 2.0 - - - -
101B TRP* 3.6 7.3 - - - -
102B ALA* 1.3 75.5 - - - +
104B LYS* 1.3 64.9 + - - -
105B ARG 3.4 2.1 + - - -
125B PRO* 4.4 0.9 - - - -
126B GLY 3.0 29.3 + - - +
9C SER* 3.5 22.4 + - - -
10C GLY* 4.4 2.5 - - - -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PHE* 2.8 27.5 + - + +
82B ARG 3.4 16.4 - - - +
83B GLU* 3.4 3.1 - - - +
84B ALA 2.9 35.8 + - - +
85B ASN* 3.0 10.9 + - - +
103B GLY* 1.3 72.2 - - - -
105B ARG* 1.3 58.6 + - - +
124B GLY 3.6 7.0 - - - +
125B PRO* 4.0 19.3 - - + -
9C SER* 3.3 13.6 + - - +
40C THR* 4.1 20.6 - - + +
68C VAL* 4.5 1.3 - - + +
70C GLN* 4.7 0.9 - - - -
72C ASN 3.1 16.1 + - - -
73C ASP* 2.8 24.9 + - - +
75C GLU* 2.8 28.4 + - - +
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ARG 4.3 2.1 + - - -
83B GLU* 3.7 8.3 - - - +
85B ASN* 3.4 24.5 - - - +
87B GLN* 4.1 20.2 + - - +
101B TRP* 3.1 62.8 - - + +
103B GLY 3.4 0.4 + - - -
104B LYS* 1.3 76.7 - - - +
106B PHE* 1.3 81.1 + - - +
107B TYR* 3.0 21.8 + - - +
108B GLN* 5.3 4.6 - - - +
123B SER* 3.5 0.5 - - - -
124B GLY 3.2 29.0 + - - +
130B GLU* 2.8 36.3 + - - -
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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