Contacts of the strand formed by residues 85 - 101 (chain A) in PDB entry 3MOK
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 LEU 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.8 27.4 - - + -
56A TYR* 4.7 3.4 - - + -
73A LEU* 4.1 14.8 - - + -
74A HIS 3.2 9.9 - - - +
75A TYR* 3.9 10.0 - - + -
84A THR* 1.3 72.2 - - - +
86A TRP* 1.3 62.0 + - - +
123A SER* 5.6 0.2 - - - -
133A VAL* 3.8 20.6 - - + +
134A HIS* 3.0 49.5 + - + +
137A VAL* 3.8 28.0 - - + -
138A TYR 5.4 0.2 - - - +
141A MET* 3.6 31.4 - - + -
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Residues in contact with TRP 86 (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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73A LEU* 3.5 6.4 - - - +
74A HIS* 2.9 83.6 + + + +
75A TYR 4.7 0.4 - - - +
76A THR* 3.5 31.8 - - + +
84A THR* 3.7 14.6 - - + -
85A LEU* 1.3 75.2 - - - +
87A GLY* 1.3 73.8 + - - +
123A SER* 3.6 20.2 - - - +
124A PRO* 4.4 9.4 - - + +
125A ILE* 3.6 43.3 - - + +
128A GLY 5.6 0.7 - - - +
133A VAL* 4.2 10.8 - - - -
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP 3.4 7.2 - - - -
73A LEU* 4.6 0.9 - - - -
74A HIS* 4.1 3.8 - - - -
86A TRP* 1.3 91.4 - - - +
88A LYS* 1.3 61.4 + - - -
122A ASP* 3.3 9.8 - - - -
123A SER 2.9 33.7 + - - -
133A VAL* 3.5 9.1 - - - +
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Residues in contact with LYS 88 (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 GLY* 3.2 4.9 - - - -
72A ASP* 2.8 59.3 + - + +
73A LEU* 3.3 8.8 - - - +
87A GLY* 1.3 72.1 - - - -
89A LEU* 1.3 60.1 + - - +
90A ASP* 3.9 13.0 - - - +
121A LEU 3.4 6.5 - - - +
122A ASP* 3.5 32.1 + - + +
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Residues in contact with LEU 89 (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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69A ALA* 3.8 21.8 - - + -
70A GLY 3.7 7.0 - - - +
73A LEU* 4.4 6.3 - - + -
87A GLY 3.8 1.2 + - - -
88A LYS* 1.3 72.5 - - - +
90A ASP* 1.3 60.5 + - - +
91A SER 3.4 24.0 - - - +
92A ILE* 3.9 8.1 - - + -
119A LEU* 3.7 10.8 - - + +
120A GLY 3.9 0.2 + - - -
121A LEU* 2.8 50.3 + - + +
133A VAL* 3.9 22.4 - - + -
136A VAL* 3.8 31.0 - - + -
137A VAL* 4.0 14.1 - - + -
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Residues in contact with ASP 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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70A GLY 2.8 13.7 + - - +
71A GLY* 3.6 18.0 - - - -
88A LYS* 3.9 11.6 - - - +
89A LEU* 1.3 79.6 + - - +
91A SER* 1.3 59.3 + - - +
118A ASN* 3.1 17.1 + - - +
119A LEU* 3.0 28.7 + - - +
120A GLY* 4.8 7.5 + - - +
121A LEU 5.2 1.0 - - - +
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Residues in contact with SER 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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68A ILE 4.9 1.6 + - - -
69A ALA* 3.4 4.9 - - - -
70A GLY* 2.9 41.7 + - - -
89A LEU* 3.4 7.6 - - - +
90A ASP* 1.3 80.6 - - - +
92A ILE* 1.3 65.8 + - - +
93A ALA* 4.3 0.7 - - - -
115A SER* 4.8 3.4 - - - -
116A PHE 3.1 11.7 - - - -
117A SER* 3.9 15.9 - - - -
119A LEU* 3.9 3.1 - - - +
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Residues in contact with ILE 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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67A PHE* 4.7 2.9 - - + -
68A ILE 3.5 3.4 - - - +
69A ALA* 3.6 25.1 - - + +
89A LEU* 3.9 15.3 - - + -
91A SER* 1.3 81.5 - - - +
93A ALA* 1.3 62.8 + - - +
94A LEU* 3.6 30.3 - - + -
115A SER* 3.4 2.7 - - - -
116A PHE* 2.8 42.1 + - + +
119A LEU* 3.9 14.3 - - + +
136A VAL* 4.4 0.7 - - + -
137A VAL* 4.5 3.8 - - + -
140A LEU* 3.9 24.0 - - + -
148A LEU* 4.1 25.4 - - + -
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Residues in contact with ALA 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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67A PHE* 3.2 7.3 - - - +
68A ILE* 2.9 43.4 + - + +
91A SER* 4.3 1.3 - - - +
92A ILE* 1.3 73.3 - - - +
94A LEU* 1.3 62.1 + - - +
109A LEU* 3.7 18.5 - - + +
112A GLN* 3.8 21.5 - - - +
114A VAL 3.6 4.3 - - - -
115A SER* 4.1 8.1 - - - +
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Residues in contact with LEU 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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19A TYR* 3.5 25.4 - - + +
20A LEU* 3.4 32.3 - - + -
23A TRP* 3.9 31.2 - - + +
66A ALA 3.7 1.6 - - - -
67A PHE* 3.5 25.8 - - + -
92A ILE* 3.6 18.8 - - + -
93A ALA* 1.3 73.5 - - - +
95A GLY* 1.3 59.7 + - - +
109A LEU* 3.7 5.0 - - - +
112A GLN* 3.9 1.2 - - - -
113A GLU* 2.9 21.5 + - - +
114A VAL 2.8 21.5 + - - +
116A PHE* 4.0 10.8 - - + -
140A LEU* 4.5 5.2 - - + -
148A LEU* 4.2 5.4 - - + -
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Residues in contact with GLY 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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23A TRP* 3.2 10.8 + - - +
26A TYR* 5.2 0.9 - - - -
65A ALA* 3.5 3.1 - - - -
66A ALA 2.9 30.3 + - - +
94A LEU* 1.3 76.2 - - - +
96A ASP* 1.3 61.3 + - - -
109A LEU* 3.8 6.9 - - - +
111A SER 3.2 13.7 - - - -
113A GLU* 3.7 18.6 - - - +
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Residues in contact with ASP 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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26A TYR* 2.7 35.7 + - + -
33A ARG* 4.6 2.3 + - - -
36A GLN* 3.8 12.9 - - - +
64A ASP* 3.4 13.8 - - - +
95A GLY* 1.3 74.2 - - - +
97A THR* 1.3 97.3 + - - +
109A LEU* 4.1 1.2 - - - +
110A ASP* 3.6 1.0 - - - +
111A SER* 2.9 35.9 + - - -
113A GLU* 3.8 12.3 - - - +
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Residues in contact with THR 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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39A ASP* 5.5 0.5 + - - -
40A GLY* 4.6 7.4 - - - -
59A LYS* 5.1 3.1 - - - -
64A ASP* 2.8 32.7 + - - +
66A ALA* 4.0 5.3 - - - +
96A ASP* 1.3 90.9 + - - +
98A LEU* 1.3 64.2 + - - +
99A THR* 5.1 0.2 - - + -
109A LEU* 3.3 6.8 - - - +
110A ASP* 2.8 44.1 + - + +
186A PO4 3.5 32.1 - - - +
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Residues in contact with LEU 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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42A ASN* 3.5 31.0 + - - +
43A THR 3.7 7.0 - - - -
44A GLY* 3.5 36.8 - - - +
57A ALA* 4.0 8.5 - - + -
58A LEU 3.8 18.4 - - - +
59A LYS* 3.9 2.5 - - + +
66A ALA* 3.8 11.9 - - + +
67A PHE 4.2 1.1 - - - +
68A ILE* 3.8 26.5 - - + -
97A THR* 1.3 74.6 - - - +
99A THR* 1.3 59.0 + - - +
107A TYR* 4.7 3.8 - - + -
108A ALA 3.4 12.6 - - - +
109A LEU* 3.9 11.9 - - + -
186A PO4 2.6 28.1 + - - -
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Residues in contact with THR 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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42A ASN* 3.6 3.8 - - - +
98A LEU* 1.3 80.2 - - - +
100A GLY* 1.3 67.4 + - - +
107A TYR* 3.4 6.6 - - - -
108A ALA* 2.8 47.2 + - - +
109A LEU 4.9 0.7 + - - -
110A ASP* 4.2 26.5 - - + +
186A PO4 3.8 11.2 - - - +
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Residues in contact with GLY 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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42A ASN* 2.8 26.8 + - - +
99A THR* 1.3 78.2 - - - +
101A GLY* 1.3 58.7 + - - -
104A SER* 4.1 20.4 - - - -
106A GLY 3.5 9.2 - - - -
107A TYR* 3.7 2.0 - - - -
108A ALA* 5.9 0.2 - - - -
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Residues in contact with GLY 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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47A ASN* 4.8 0.2 - - - -
100A GLY* 1.3 75.2 - - - -
102A ALA* 1.3 67.3 + - - -
103A SER 3.2 2.7 - - - -
104A SER* 3.1 9.0 + - - -
106A GLY* 2.9 31.8 + - - -
107A TYR* 3.7 23.1 - - - +
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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