Contacts of the strand formed by residues 105 - 113 (chain B) in PDB entry 1MS4
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 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 5.1 0.7 - - - -
100B ILE 3.7 0.7 - - - +
101B VAL* 3.5 9.7 - - - +
102B LYS 3.0 33.5 + - - +
103B GLY 3.3 0.6 - - - -
104B ASN* 1.3 80.8 - - + +
106B LEU* 1.3 63.2 + - - +
107B TYR* 3.2 36.9 + - + +
135B VAL* 4.0 12.6 - - + -
136B GLY 3.4 2.7 - - - +
137B GLU* 2.0 52.2 + - - +
213B GLU* 6.4 0.7 - - - -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.8 20.2 - - + -
42B VAL* 3.6 25.6 - - + -
47B VAL* 4.3 6.3 - - + -
49B ILE* 4.3 9.9 - - + -
99B VAL* 4.2 13.2 - - + -
100B ILE 3.6 1.8 - - - -
101B VAL* 4.5 2.9 - - + -
105B LYS* 1.3 72.9 - - - +
107B TYR* 1.3 62.7 + - - +
108B VAL* 3.9 3.1 - - + -
134B ALA 3.4 1.7 - - - +
135B VAL* 3.0 9.0 - - - +
136B GLY 2.7 35.8 + - - +
138B VAL* 3.7 26.2 - - + -
151B ILE* 4.0 20.9 - - + -
153B TRP* 4.0 25.0 - - + -
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.3 2.9 - - - +
100B ILE* 2.7 58.4 + - + +
102B LYS* 4.1 18.8 - - + +
105B LYS* 3.2 43.3 - - + +
106B LEU* 1.3 74.3 - - - +
108B VAL* 1.3 57.6 + - - +
133B LEU* 4.2 17.0 - - + -
134B ALA 3.7 2.5 - - - -
135B VAL* 4.1 24.7 - - + -
190B LEU* 3.7 24.7 - - + -
192B TYR* 2.9 17.8 + - + +
213B GLU* 3.4 38.7 + - - +
214B GLY* 4.8 0.4 - - - -
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE* 4.2 14.8 - - + -
65B THR* 4.6 7.0 - - + -
82B ALA* 5.6 0.4 - - + -
83B ILE* 3.7 25.0 - - + +
97B PRO* 4.1 25.6 - - + -
98B THR 3.2 4.7 - - - +
99B VAL* 4.4 7.2 - - + -
106B LEU* 4.5 4.5 - - + +
107B TYR* 1.3 75.8 - - - +
109B LEU* 1.3 60.2 + - - +
110B VAL* 4.0 1.9 + - + -
132B LEU 3.7 1.4 - - - +
133B LEU* 3.5 5.6 - - - +
134B ALA* 2.9 37.6 + - - +
153B TRP* 3.6 34.3 - - + -
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Residues in contact with LEU 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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96B ASP 3.4 3.5 - - - +
97B PRO* 3.4 3.8 - - - +
98B THR* 2.7 38.0 + - - +
108B VAL* 1.3 71.6 - - - +
110B VAL* 1.3 60.9 + - - +
131B ILE* 3.6 28.3 - - + -
132B LEU 3.5 15.0 - - - +
133B LEU* 4.2 4.7 - - + -
159B LEU* 4.0 22.4 - - + -
175B PHE* 4.9 0.7 - - + -
177B GLY* 3.9 27.2 + - - +
192B TYR* 3.4 44.9 + - + -
194B VAL* 4.4 7.4 - - + -
208B PHE* 4.5 6.5 - - + -
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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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65B THR* 3.8 15.5 - - - +
83B ILE* 3.9 21.5 - - + -
94B VAL* 3.8 22.9 - - + -
95B VAL 3.3 20.4 - - - +
96B ASP 4.6 0.2 - - - -
97B PRO* 3.5 22.2 - - + -
108B VAL* 4.4 0.7 - - + -
109B LEU* 1.3 80.5 - - - +
111B GLY* 1.3 64.9 + - - +
131B ILE* 3.4 6.4 - - - +
132B LEU* 2.8 47.4 + - + +
177B GLY 5.9 1.3 - - - +
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Residues in contact with GLY 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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94B VAL* 3.0 6.6 - - - +
95B VAL* 2.9 39.9 + - - +
110B VAL* 1.3 76.8 - - - +
112B SER* 1.3 59.3 + - - -
113B TYR* 4.4 1.3 - - - -
130B ASP 3.5 7.6 - - - -
131B ILE* 4.0 3.1 - - - +
176B LEU* 3.5 31.0 - - - +
177B GLY 5.7 0.4 - - - +
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Residues in contact with SER 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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86B SER* 4.9 9.4 + - - -
93B ARG 3.3 8.2 + - - -
94B VAL* 3.9 6.6 - - - +
111B GLY* 1.3 74.4 - - - -
113B TYR* 1.3 67.4 + - - +
114B ASN* 4.8 6.7 + - - -
128B ASP 3.4 5.7 - - - +
129B TRP* 3.4 1.7 - - - -
130B ASP* 2.8 47.6 + - - +
132B LEU* 3.7 30.3 - - - +
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Residues in contact with TYR 113 (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 ASN* 5.1 0.5 - - - +
86B SER* 4.3 1.6 + - - -
91B VAL 4.9 0.4 - - - -
92B SER* 3.4 3.2 - - - -
93B ARG* 3.0 67.4 + - + +
95B VAL* 3.7 31.2 - - + -
112B SER* 1.3 81.0 + - - +
114B ASN* 1.3 66.1 + - - +
116B SER* 3.9 6.5 - - - -
120B TRP* 3.2 22.3 - - + +
123B HIS* 4.1 7.0 - + - -
128B ASP* 3.3 27.8 - - - +
129B TRP* 3.2 22.5 - + + -
174B GLN* 2.8 34.6 + - - -
176B LEU* 3.7 14.4 - - + +
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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