Contacts of the strand formed by residues 101 - 113 (chain A) in PDB entry 4MOB
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A THR* 5.0 6.9 + - - -
92A MET* 3.6 36.4 - - + +
93A VAL 3.1 3.9 - - - +
94A GLN* 3.8 38.1 + - + +
99A GLY 3.6 2.3 + - - +
100A ILE* 1.3 76.4 - - - +
102A LYS* 1.3 67.0 + - - +
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Residues in contact with LYS 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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63A GLU* 3.5 43.4 + - + +
92A MET* 3.3 9.3 - - - +
93A VAL* 2.9 40.4 + - + +
100A ILE* 4.4 17.9 - - + +
101A GLU* 1.3 78.7 - - - +
103A LEU* 1.3 62.9 + - - +
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Residues in contact with LEU 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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62A GLU* 3.4 29.9 - - + +
63A GLU* 3.5 11.1 - - - +
90A LYS* 4.0 12.3 - - + -
91A VAL 3.8 12.3 - - - +
92A MET* 3.5 22.3 - - + +
102A LYS* 1.3 72.5 - - - +
104A VAL* 1.3 59.5 + - - +
105A SER 3.9 9.4 - - - +
106A VAL* 3.7 33.0 - - + +
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Residues in contact with VAL 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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31A LEU* 4.2 15.5 - - + -
61A PHE* 3.4 19.7 - - + -
62A GLU* 2.6 34.5 + - - +
63A GLU* 3.8 26.2 - - + +
65A ALA* 5.4 3.8 - - + +
71A ILE* 4.5 4.3 - - + -
91A VAL* 2.7 26.9 + - + +
92A MET 3.9 2.5 - - - -
93A VAL* 3.6 42.4 - - + +
103A LEU* 1.3 74.8 - - - +
105A SER* 1.3 61.1 + - - +
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Residues in contact with SER 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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59A ILE* 3.3 25.7 - - - +
60A GLN 2.9 20.1 + - - -
61A PHE* 4.3 8.1 - - - -
62A GLU* 4.8 3.1 - - - -
89A ILE 4.6 0.4 - - - -
90A LYS* 3.6 2.1 - - - -
91A VAL* 2.8 40.6 + - - +
103A LEU* 3.7 5.6 - - - +
104A VAL* 1.3 91.2 - - - +
106A VAL* 1.3 69.2 + - - +
107A ALA* 4.4 1.0 - - - +
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Residues in contact with VAL 106 (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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58A ASP 4.8 4.9 - - - +
60A GLN 4.8 4.4 + - - -
88A SER* 6.5 0.7 - - - -
89A ILE 3.4 8.5 - - - +
90A LYS* 4.4 14.6 - - + -
103A LEU* 3.7 29.1 - - + +
105A SER* 1.3 81.7 + - - +
107A ALA* 1.3 65.0 + - - +
108A PHE* 5.2 12.5 - - + -
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Residues in contact with ALA 107 (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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35A ILE* 5.5 2.9 - - + -
56A VAL* 6.0 2.7 - - + -
57A ASP 6.0 0.2 - - - +
58A ASP 4.7 4.9 - - - +
59A ILE* 4.0 34.1 - - + -
88A SER* 3.4 4.7 - - - -
89A ILE* 2.8 48.8 + - + +
105A SER* 4.4 1.6 - - - +
106A VAL* 1.3 77.1 - - - +
108A PHE* 1.3 71.0 + - - +
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Residues in contact with PHE 108 (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 VAL* 3.8 5.0 - - - +
57A ASP* 2.9 42.0 + - + +
78A THR* 4.7 0.4 - - + -
86A GLU* 3.6 19.1 - - + -
87A ILE 3.2 7.2 - - - +
88A SER* 3.4 31.0 - - - -
89A ILE* 4.1 1.6 - - - -
106A VAL* 5.2 11.4 - - + -
107A ALA* 1.3 80.9 - - - +
109A SER* 1.3 62.5 + - - +
136A GLU* 4.1 7.4 - - - -
143A ARG* 3.3 50.0 - - - -
147A ARG* 3.5 20.0 - - - +
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Residues in contact with SER 109 (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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35A ILE* 6.1 1.8 - - - -
36A ASP* 4.7 2.0 + - - -
39A ALA* 4.6 2.2 - - - -
53A THR* 3.9 8.3 - - - +
55A SER 3.1 17.2 + - - -
56A VAL* 4.0 10.7 - - - +
57A ASP* 4.6 0.9 - - - +
86A GLU* 3.7 2.4 - - - +
87A ILE* 2.7 34.7 + - - +
89A ILE* 3.9 17.0 - - - +
108A PHE* 1.3 76.1 - - - +
110A THR* 1.3 60.7 + - - +
111A PHE* 3.4 25.0 - - - -
147A ARG* 5.6 0.4 - - - -
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Residues in contact with THR 110 (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 THR* 3.8 0.5 - - - -
54A ALA* 2.8 29.8 + - + -
55A SER* 2.8 32.5 + - - +
57A ASP* 5.6 0.4 + - - -
81A PHE* 6.1 2.2 - - + -
84A SER* 4.1 12.3 - - - +
85A MET 3.4 12.0 + - - +
86A GLU* 4.6 2.6 - - - +
109A SER* 1.3 75.1 + - - +
111A PHE* 1.3 74.6 + - - +
147A ARG* 3.7 28.1 + - - -
401A COA 3.6 22.0 - - + +
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Residues in contact with PHE 111 (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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36A ASP* 3.4 25.6 - - - -
39A ALA* 3.5 19.5 - - + -
40A CYS* 3.4 38.4 - - + -
43A ALA* 3.6 22.0 - - + -
51A CYS* 4.1 8.1 - - + -
52A VAL* 3.3 25.6 - - - -
53A THR* 3.4 18.6 - - + -
83A THR 4.0 0.2 - - - +
84A SER* 3.2 4.7 - - - -
85A MET* 2.8 36.8 + - + +
87A ILE* 3.9 16.6 - - + -
109A SER* 3.4 21.1 - - - -
110A THR* 1.3 78.4 - - - +
112A VAL* 1.3 61.9 + - - +
113A ALA 4.4 0.2 + - - -
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Residues in contact with VAL 112 (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 CYS* 3.3 3.0 - - - -
52A VAL* 2.9 40.4 + - + +
54A ALA* 3.7 22.4 - - + +
83A THR* 3.5 15.0 - - - +
84A SER* 4.0 12.6 - - - -
111A PHE* 1.3 74.4 - - - +
113A ALA* 1.3 76.5 + - - +
114A LYS* 3.5 18.8 + - - +
401A COA 3.8 38.1 - - + +
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Residues in contact with ALA 113 (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 ALA* 4.3 6.7 - - + -
49A VAL* 3.7 20.4 - - + -
50A SER 3.8 4.3 - - - -
51A CYS* 3.8 12.0 - - - -
83A THR* 2.9 19.8 + - - +
85A MET* 4.5 1.7 - - + +
111A PHE 4.4 0.2 + - - -
112A VAL* 1.3 82.3 - - - +
114A LYS* 1.3 61.8 + - - +
115A PRO* 3.2 9.4 - - - +
121A ILE* 4.0 25.1 - - + +
123A LEU* 4.4 4.0 - - + -
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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