Contacts of the strand formed by residues 101 - 114 (chain B) in PDB entry 4MT5
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 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B TYR 3.8 6.0 + - - +
95B VAL* 4.4 5.3 - - - +
99B ASN 4.2 0.8 + - - -
100B GLN* 1.3 71.3 + - - +
102B VAL* 1.3 62.3 + - - +
103B GLN 4.0 21.5 - - - +
104B PRO* 4.9 1.8 - - + -
105B ASP* 5.3 6.2 + - - +
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Residues in contact with VAL 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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94B TYR* 3.1 25.3 + - + +
95B VAL 4.1 6.3 - - - +
96B ASP* 3.6 32.1 - - + +
100B GLN* 3.3 16.4 - - + +
101B THR* 1.3 75.1 - - - +
103B GLN* 1.3 70.7 - - + +
104B PRO* 4.9 0.2 - - - +
151B VAL* 4.7 14.5 - - + +
154B TYR* 6.4 0.4 - - + -
179B TYR* 4.2 21.3 - - + -
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 3.6 33.7 + - + +
101B THR* 3.6 12.3 - - - +
102B VAL* 1.3 85.7 - - + +
104B PRO* 1.3 82.0 - - + +
105B ASP* 3.7 2.3 + - - +
149B PRO* 3.2 38.9 - - + +
150B ALA 4.0 10.1 + - - -
151B VAL* 3.1 25.3 - - - +
179B TYR* 3.5 6.1 + - - -
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Residues in contact with PRO 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 3.0 20.4 - - - -
101B THR* 4.9 4.2 - - + -
103B GLN* 1.3 93.6 - - + +
105B ASP* 1.3 71.4 + - - +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR* 3.9 13.6 - - + +
92B ILE 3.2 11.7 - - - +
93B HIS* 3.1 38.5 + - - -
94B TYR* 4.5 1.1 + - - -
101B THR* 5.3 6.4 + - - +
103B GLN 4.3 4.5 - - - +
104B PRO* 1.3 81.6 - - - +
106B SER* 1.3 59.9 + - - +
107B THR* 3.7 9.7 + - - +
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Residues in contact with SER 106 (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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90B GLU* 3.3 9.2 + - - +
91B THR* 3.6 0.4 - - - -
92B ILE* 3.0 41.8 + - - +
94B TYR* 3.5 24.8 - - - -
104B PRO 3.6 1.0 + - - -
105B ASP* 1.3 71.6 - - - +
107B THR* 1.3 60.2 + - - +
108B THR* 4.1 7.2 + - - +
146B VAL* 3.5 27.3 - - - +
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 3.7 26.0 - - + -
90B GLU 3.3 3.1 - - - +
91B THR* 3.6 19.2 + - - +
105B ASP* 3.7 10.8 + - - +
106B SER* 1.3 73.7 + - - +
108B THR* 1.3 73.2 + - - +
109B ALA* 5.5 2.0 - - + -
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 3.6 2.6 - - - +
90B GLU* 3.0 53.2 + - - +
106B SER* 4.1 11.2 + - - +
107B THR* 1.3 80.9 - - - +
109B ALA* 1.3 60.0 + - - +
143B PHE* 3.4 21.7 - - - +
146B VAL* 5.0 6.1 - - + -
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Residues in contact with ALA 109 (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 THR* 4.8 9.2 - - + -
88B VAL 3.7 8.5 - - - +
89B THR* 4.2 16.4 - - + +
107B THR* 5.5 2.2 - - + -
108B THR* 1.3 76.4 - - - +
110B VAL* 1.3 61.7 + - - +
111B THR* 5.6 0.9 - - - +
141B LYS* 6.1 0.2 - - - -
143B PHE* 4.0 6.1 - - - -
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Residues in contact with VAL 110 (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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86B LYS 4.1 0.3 - - - +
87B THR* 3.6 1.3 - - - +
88B VAL* 2.8 43.9 + - + +
109B ALA* 1.3 75.4 - - - +
111B THR* 1.3 70.3 + - - +
112B PHE* 3.9 15.4 + - + -
133B VAL* 3.5 28.7 - - + -
141B LYS* 3.6 29.6 - - + -
143B PHE* 3.8 15.0 - - + -
166B VAL* 3.9 19.1 - - + -
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Residues in contact with THR 111 (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 GLN* 4.3 15.5 - - + +
86B LYS 3.4 9.4 - - - +
87B THR* 2.9 27.9 + - - +
109B ALA* 5.6 1.0 - - - +
110B VAL* 1.3 81.4 + - - +
112B PHE* 1.3 72.0 + - - +
113B LYS* 3.8 20.1 + - + +
132B THR 3.9 5.5 - - - +
133B VAL* 4.2 11.3 - - - +
134B ASP* 4.8 5.7 + - - +
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Residues in contact with PHE 112 (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 GLN* 3.1 28.4 - - - +
86B LYS 2.8 20.6 + - - +
88B VAL* 4.1 7.4 - - + -
110B VAL* 3.9 18.4 - - + -
111B THR* 1.3 72.6 - - - +
113B LYS* 1.3 59.7 + - - +
131B TRP* 3.4 24.0 - - + -
132B THR 3.6 2.5 - - - -
133B VAL* 3.8 27.1 - - + -
138B ALA 4.2 7.0 - - - -
140B SER* 3.8 19.7 - - - -
141B LYS* 4.1 21.1 - - + -
166B VAL* 4.2 2.7 - - + -
167B THR* 3.6 33.0 - - - -
168B PRO* 3.5 27.6 - - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA* 3.8 26.1 - - + +
79B THR* 5.5 2.6 - - - +
83B ALA* 5.0 2.0 - - + -
84B GLU 3.4 3.6 - - - +
85B GLN* 3.8 27.1 - - + +
111B THR* 4.4 15.7 - - + +
112B PHE* 1.3 80.4 - - - +
114B ARG* 1.3 60.2 - - - +
131B TRP* 3.7 2.0 - - - -
132B THR* 2.7 52.4 + - - +
134B ASP 6.2 2.9 - - - +
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Residues in contact with ARG 114 (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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78B ALA* 4.0 8.7 - - - -
83B ALA* 3.2 4.7 - - - +
84B GLU* 2.9 69.3 + - + -
113B LYS* 1.3 77.0 - - - +
115B GLY* 1.3 61.3 + - - +
128B TYR* 3.6 42.1 - - + +
129B ASP 3.4 22.6 + - - +
130B PRO 3.9 6.1 - - - +
131B TRP* 3.2 51.4 - - + +
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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