Contacts of the strand formed by residues 116 - 124 (chain B) in PDB entry 3MXN
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 CYS 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B SER* 3.3 22.0 - - - +
84B ARG* 5.5 16.2 - - + +
109B GLN* 2.8 33.3 + - + -
110B ALA* 2.9 29.4 + - + +
114B GLU* 3.3 19.7 - - - -
115B PRO* 1.3 75.4 - - - +
117B LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 117 (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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30B LEU* 4.5 5.6 - - + -
58B VAL* 3.6 27.6 - - + -
60B MET* 3.8 29.8 - - + -
81B PHE* 4.3 12.6 - - + -
82B SER 2.8 13.6 + - - +
83B VAL* 3.4 7.5 - - + -
84B ARG* 2.9 30.3 + - - +
104B VAL* 4.0 22.9 - - + +
106B GLY* 4.2 11.4 - - - +
107B VAL 3.3 5.8 - - - +
108B VAL* 3.8 18.8 - - + +
109B GLN* 4.2 3.8 - - - -
115B PRO* 5.4 1.6 - - + -
116B CYS* 1.3 83.5 - - - +
118B GLN* 1.3 60.4 + - - +
119B ALA 3.8 0.2 - - - -
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Residues in contact with GLN 118 (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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84B ARG* 3.8 20.2 - - - +
85B GLY* 3.8 21.6 - - - +
87B GLU* 5.6 0.2 + - - -
88B ARG* 5.3 7.5 - - - +
106B GLY* 3.2 1.5 - - - -
107B VAL* 2.8 41.2 + - + +
109B GLN* 3.8 30.5 - - + +
117B LEU* 1.3 72.3 - - - +
119B ALA* 1.3 68.2 + - - +
120B VAL* 3.6 2.3 + - - +
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Residues in contact with ALA 119 (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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83B VAL* 3.6 22.2 - - + -
84B ARG 2.9 20.4 + - - +
85B GLY* 4.5 5.2 - - - +
86B LEU* 3.7 18.8 - - + -
88B ARG* 5.6 2.3 - - - +
89B VAL* 3.7 16.8 - - + +
104B VAL* 4.5 5.4 - - + -
105B MET 3.8 4.5 - - - -
106B GLY* 4.3 1.8 - - - -
117B LEU 3.8 1.2 + - - -
118B GLN* 1.3 77.7 - - - +
120B VAL* 1.3 61.0 + - - +
121B LYS 4.6 1.6 - - - +
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Residues in contact with VAL 120 (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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515A VAL* 5.0 9.2 - - + +
17B LEU* 5.6 15.0 - - + +
18B PRO* 4.8 6.5 - - + -
89B VAL* 3.4 16.3 - - - +
90B PRO* 3.6 8.0 - - - +
105B MET* 2.7 48.2 + - + +
106B GLY* 4.5 2.9 - - - -
107B VAL* 4.2 25.1 - - + -
118B GLN 4.3 1.8 - - - +
119B ALA* 1.3 77.0 - - - +
121B LYS* 1.3 65.1 + - + +
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Residues in contact with LYS 121 (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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513A PHE* 4.0 23.3 - - + +
514A ILE* 2.8 33.3 + - - +
515A VAL* 3.9 14.8 - - - +
585A LEU 4.5 0.6 + - - -
586A ILE* 2.8 41.0 + - - +
588A LEU 5.0 0.6 + - - -
89B VAL* 4.1 9.4 - - - -
90B PRO* 4.5 15.5 - - + -
103B MET* 4.4 5.8 - - - -
104B VAL* 3.2 9.9 - - - +
105B MET* 3.0 37.5 + - + +
119B ALA* 4.6 1.1 - - - +
120B VAL* 1.3 89.6 + - + +
122B MET* 1.3 60.1 + - - +
123B THR* 3.9 14.6 + - + +
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Residues in contact with MET 122 (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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64B VAL* 5.0 0.7 - - - -
72B ALA* 4.4 0.2 - - + -
74B LEU* 4.0 24.0 - - + -
83B VAL* 4.6 2.5 - - + -
86B LEU* 3.7 38.8 - - + -
89B VAL* 4.1 11.1 - - + +
90B PRO 4.5 9.6 + - - +
92B GLY* 5.5 1.6 + - - -
95B CYS* 4.0 22.8 - - - +
96B LEU* 3.8 25.6 - - + -
102B VAL* 4.0 18.4 - - + -
103B MET 3.2 11.9 - - - +
104B VAL* 3.6 19.5 - - + -
121B LYS* 1.3 75.5 - - - +
123B THR* 1.3 68.9 + - - +
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Residues in contact with THR 123 (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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513A PHE* 6.1 0.9 - - - +
586A ILE* 3.3 37.3 + - + +
587A ASP* 3.5 25.4 + - - +
588A LEU 5.5 1.2 + - - -
589A CYS* 5.5 1.2 - - - +
90B PRO 5.3 0.7 - - - +
92B GLY 5.5 0.9 - - - +
93B ARG 5.7 0.4 - - - -
95B CYS* 3.7 7.0 - - - -
102B VAL* 3.3 3.5 - - - +
103B MET* 3.0 50.2 + - - +
121B LYS* 3.9 16.7 + - + -
122B MET* 1.3 82.0 - - - +
124B ASP* 1.3 63.3 + - - +
125B LEU* 4.2 2.8 - - - +
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Residues in contact with ASP 124 (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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587A ASP* 4.2 13.8 + - - +
93B ARG* 3.4 48.9 + - + +
94B PRO 4.4 2.6 - - - +
95B CYS* 3.6 27.0 - - + +
100B LYS* 3.4 26.0 + - - +
101B TYR 3.2 4.3 - - - +
102B VAL* 4.1 0.3 - - - +
123B THR* 1.3 74.5 + - - +
125B LEU* 1.3 71.3 + - - +
126B SER* 2.6 30.4 + - - -
127B ASP* 4.9 0.7 - - - +
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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