Contacts of the strand formed by residues 67 - 76 (chain A) in PDB entry 1MOL
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 LYS 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TYR* 4.1 21.6 + - - +
32A LEU* 5.3 3.7 - - + +
62A VAL 3.5 1.2 - - - +
63A TYR* 3.2 5.3 - - - -
64A ALA 3.0 27.0 + - - +
65A SER* 3.7 15.5 - - - +
66A ASP* 1.3 79.5 - - - +
68A LEU* 1.3 59.7 + - - +
69A PHE* 3.5 33.3 - - + -
90A PRO* 3.5 31.2 - - + +
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Residues in contact with LEU 68 (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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38A ILE* 3.9 25.1 - - + -
61A TYR* 4.1 5.2 - - + -
62A VAL 3.6 28.3 - - - +
63A TYR* 3.7 32.4 - - + +
67A LYS* 1.3 71.8 - - - +
69A PHE* 1.3 61.8 + - - +
90A PRO* 3.1 11.2 - - - +
91A VAL* 2.8 47.9 + - + +
92A PRO 4.0 2.9 - - - +
93A PRO* 3.6 38.1 - - + -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.7 28.9 - + - -
32A LEU* 4.3 12.6 - - + -
61A TYR* 3.4 4.9 - - - +
62A VAL* 2.8 42.0 + - + +
64A ALA* 3.6 21.1 - - + -
67A LYS* 3.5 52.3 - - + -
68A LEU* 1.3 75.7 - - - +
70A ARG* 1.3 62.4 + - - +
71A ALA 4.1 0.2 + - - -
87A PHE* 3.4 39.0 - + + -
88A ASN 3.4 5.4 - - - +
89A GLY* 3.7 27.1 - - - -
90A PRO 4.2 1.1 - - - -
91A VAL* 4.0 2.0 - - - -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 3.6 25.6 + - - +
60A LEU 3.1 28.8 + - - +
61A TYR* 3.5 43.9 + - + -
69A PHE* 1.3 72.1 - - - +
71A ALA* 1.3 72.1 + - - +
72A ASP* 2.9 35.6 + - - -
86A ARG* 4.0 2.8 - - - +
87A PHE* 3.4 2.0 - - - -
88A ASN* 2.9 38.0 + - + +
91A VAL* 3.8 16.3 - - + +
61B TYR* 5.8 1.4 + - - -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.8 29.6 - - + -
58A TYR 3.7 0.9 - - - +
59A GLN* 3.6 0.2 - - - -
60A LEU* 2.8 37.3 + - + +
62A VAL* 4.1 15.0 - - + -
69A PHE 4.1 0.8 + - - -
70A ARG* 1.3 75.8 + - - +
72A ASP* 1.3 62.1 - - - +
73A ILE* 4.9 2.5 - - + -
84A LEU* 4.4 1.8 - - + -
86A ARG 3.3 6.5 - - - +
87A PHE* 3.8 15.0 - - + +
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Residues in contact with ASP 72 (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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57A GLU* 5.5 4.3 - - + +
58A TYR 3.2 4.0 - - - +
59A GLN* 3.3 19.7 + - + +
70A ARG* 2.9 38.7 + - - -
71A ALA* 1.3 74.6 - - - +
73A ILE* 1.3 59.3 + - - +
84A LEU* 3.8 1.6 - - - +
85A LEU* 2.8 36.3 + - + +
86A ARG* 2.9 55.6 + - + +
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Residues in contact with ILE 73 (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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15A LEU* 3.3 54.3 - - + +
18A PHE* 3.9 24.9 - - + -
19A ALA* 4.0 11.7 - - + -
57A GLU* 3.0 6.1 - - - +
58A TYR* 2.8 41.9 + - + +
60A LEU* 4.4 14.4 - - + -
71A ALA* 4.9 1.8 - - + -
72A ASP* 1.3 80.9 - - - +
74A SER* 1.3 69.6 + - - +
82A ARG* 4.3 5.4 - - + -
83A LYS 3.4 10.1 - - - +
84A LEU* 4.4 11.0 - - + -
85A LEU* 4.4 3.6 - - - -
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Residues in contact with SER 74 (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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56A TYR 3.3 9.4 - - - -
57A GLU* 4.2 4.9 - - - -
73A ILE* 1.3 76.3 - - - +
75A GLU* 1.3 63.7 + - - +
81A GLY 4.2 0.7 - - - -
82A ARG* 3.0 7.8 - - - +
83A LYS* 2.9 54.6 + - - +
85A LEU* 3.6 25.9 - - - +
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Residues in contact with GLU 75 (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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11A PHE* 4.6 2.3 - - - -
55A GLY* 3.2 2.1 - - - -
56A TYR* 2.8 49.9 + - + +
58A TYR* 3.3 34.1 + - + -
74A SER* 1.3 77.3 - - - +
76A ASP* 1.3 66.9 + - - +
80A ARG* 3.9 38.9 + - - +
81A GLY 3.2 3.6 - - - +
82A ARG* 2.9 41.2 + - + -
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Residues in contact with ASP 76 (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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54A LYS* 3.7 15.3 - - - +
55A GLY* 4.4 0.7 - - - -
74A SER 4.2 0.2 - - - -
75A GLU* 1.3 74.4 - - - +
77A TYR* 1.3 59.3 + - - +
78A LYS* 3.1 15.0 + - - +
79A THR* 3.0 44.4 + - - +
80A ARG* 2.8 31.7 + - - -
81A GLY* 2.9 13.7 + - - +
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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