Contacts of the helix formed by residues 89 - 100 (chain A) in PDB entry 3M5B
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 GLU 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A SER* 4.2 9.9 + - - -
70A THR* 5.4 1.0 + - - -
73A GLN* 3.0 28.7 + - - +
84A GLU 4.9 0.5 - - - +
85A LEU* 3.7 17.5 - - + +
86A GLN* 2.7 50.6 + - + +
88A GLY* 1.3 79.5 - - - +
90A LEU* 1.3 64.0 + - - +
91A ARG 3.5 0.7 - - - -
92A PRO* 3.4 8.1 - - - +
93A LEU* 3.4 21.7 + - - +
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Residues in contact with LEU 90 (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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6A ILE* 4.8 17.0 - - + -
8A LEU* 4.4 6.1 - - + -
85A LEU* 3.6 24.3 - - + +
86A GLN 3.9 2.4 + - - +
87A PRO* 3.6 13.1 + - + +
88A GLY 3.5 1.2 - - - -
89A GLU* 1.3 77.8 - - - +
91A ARG* 1.3 58.2 + - - +
93A LEU* 3.2 4.0 + - - +
94A GLN* 2.9 29.5 + - - +
109A CYS* 3.8 34.6 - - + +
112A ALA* 3.9 17.7 - - + +
113A ARG* 3.8 43.3 - - + +
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Residues in contact with ARG 91 (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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87A PRO 4.9 1.4 + - - -
88A GLY 4.7 1.0 + - - +
90A LEU* 1.3 76.8 - - - +
92A PRO* 1.3 70.1 - - + +
93A LEU 3.2 0.2 + - - -
94A GLN* 3.3 5.4 + - - +
95A GLU* 3.0 48.4 + - + +
113A ARG* 3.7 36.8 - - - +
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Residues in contact with PRO 92 (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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70A THR* 3.7 21.5 - - + +
88A GLY 3.4 19.7 - - - +
89A GLU* 3.4 13.9 - - - +
91A ARG* 1.3 95.3 - - + +
93A LEU* 1.3 54.6 + - - +
95A GLU* 3.5 13.0 + - - +
96A ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 93 (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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8A LEU* 3.9 17.9 - - + -
70A THR* 3.7 32.0 - - + +
73A GLN* 4.0 18.4 - - + +
74A LEU* 3.9 12.6 - - + +
77A PHE* 6.3 0.2 - - + -
83A VAL* 4.5 4.9 - - + -
85A LEU* 3.9 18.2 - - + -
89A GLU 3.4 10.5 + - - +
90A LEU 3.2 10.2 + - - +
92A PRO* 1.3 74.9 - - - +
94A GLN* 1.3 60.8 + - - +
96A ALA* 3.3 3.9 + - + +
97A ALA* 2.8 31.7 + - - +
105A LEU* 3.7 38.1 - - + -
109A CYS* 4.0 4.7 - - - -
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Residues in contact with GLN 94 (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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90A LEU 2.9 15.8 + - - +
91A ARG* 3.6 6.5 - - + +
93A LEU* 1.3 76.5 - - - +
95A GLU* 1.3 58.5 + - + +
97A ALA* 3.3 5.4 + - - +
98A ARG* 2.9 29.4 + - + +
106A GLU* 3.9 29.8 + - + +
109A CYS* 3.7 12.0 - - + -
110A TRP* 3.7 32.8 + - - +
113A ARG* 3.1 44.0 + - - +
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Residues in contact with GLU 95 (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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66A ILE* 5.9 0.2 - - - -
91A ARG* 3.0 44.5 + - + +
92A PRO* 3.8 10.1 - - - +
94A GLN* 1.3 74.7 - - + +
96A ALA* 1.3 63.2 + - - +
98A ARG* 3.6 8.8 + - - +
99A ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 96 (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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66A ILE* 4.1 32.5 - - + -
70A THR* 3.7 20.2 - - + -
71A PHE* 6.0 0.2 - - - -
74A LEU* 4.1 14.1 - - + -
92A PRO 3.0 18.2 + - - +
93A LEU* 3.3 4.9 + - + +
95A GLU* 1.3 75.0 - - - +
97A ALA* 1.3 63.2 + - - +
99A ALA* 3.3 1.6 + - - -
100A LEU* 3.1 29.1 + - - +
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Residues in contact with ALA 97 (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 LEU* 4.0 9.5 - - - +
93A LEU 2.8 20.3 + - - +
94A GLN 3.8 3.6 - - - +
96A ALA* 1.3 73.6 - - - +
98A ARG* 1.3 61.0 + - - +
100A LEU 3.8 0.4 - - - +
101A GLY* 3.1 4.5 + - - -
102A VAL* 2.9 48.9 + - + +
105A LEU* 3.8 18.8 - - + -
106A GLU* 3.7 17.8 - - - +
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Residues in contact with ARG 98 (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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53A GLN* 5.4 0.2 + - - -
94A GLN* 2.9 16.7 + - + +
95A GLU* 3.7 9.6 - - - +
97A ALA* 1.3 74.7 - - - +
99A ALA* 1.3 64.5 + - - +
101A GLY* 3.3 11.3 + - - -
106A GLU* 3.5 34.8 - - - +
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Residues in contact with ALA 99 (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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53A GLN* 3.3 21.3 + - - +
64A GLU* 3.3 30.1 - - - +
66A ILE* 4.8 2.9 - - + -
95A GLU 3.1 18.0 + - - +
96A ALA* 3.9 5.4 - - - +
98A ARG* 1.3 79.6 - - - +
100A LEU* 1.3 61.5 + - + +
101A GLY 3.4 0.7 - - - -
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Residues in contact with LEU 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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51A SER* 2.7 28.2 + - - -
53A GLN* 3.6 23.5 + - - +
54A LEU* 3.9 30.8 - - + +
60A TRP* 5.8 0.2 - - + -
62A LEU* 3.7 29.2 - - + -
64A GLU* 4.0 14.4 - - - +
66A ILE* 4.1 15.3 - - + -
71A PHE* 4.0 27.4 - - + -
74A LEU* 4.1 12.3 - - + -
96A ALA* 3.1 18.0 + - + +
97A ALA 4.5 1.1 - - - +
99A ALA* 1.3 76.1 - - - +
101A GLY* 1.3 54.0 + - - +
102A VAL* 3.5 8.0 + - + +
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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