Contacts of the strand formed by residues 85 - 94 (chain A) in PDB entry 3MH5
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 MET 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN* 3.6 21.1 - - + +
31A VAL 3.3 13.0 - - - +
32A GLU* 4.9 11.7 - - + -
84A PHE* 1.3 78.8 - - - +
86A ALA* 1.3 88.7 + - - +
87A LEU* 3.6 20.9 - - + -
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Residues in contact with ALA 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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31A VAL* 2.9 29.8 + - + -
84A PHE* 3.6 25.0 - - + -
85A MET* 1.3 84.1 - - - +
87A LEU* 1.3 63.0 + - - +
105A HIS 5.1 2.9 - - - +
106A VAL* 3.8 27.6 - - + +
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Residues in contact with LEU 87 (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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29A ILE 3.2 12.1 - - - +
30A ASN* 4.2 9.0 - - - +
85A MET* 3.6 17.5 - - + -
86A ALA* 1.3 81.0 - - - +
88A GLY* 1.3 59.2 + - - +
106A VAL* 3.6 11.5 - - - +
169A ASN* 4.2 22.2 - - - +
170A PRO 5.2 4.5 - - - +
171A PHE 4.3 6.3 - - - +
172A GLY* 3.5 29.4 - - - +
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Residues in contact with GLY 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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28A SER* 3.5 0.7 - - - -
29A ILE* 2.7 38.2 + - - -
87A LEU* 1.3 76.0 - - - +
89A SER* 1.3 59.6 + - - -
106A VAL* 3.6 19.7 - - - +
169A ASN* 3.3 25.0 - - - +
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Residues in contact with SER 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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26A VAL* 3.8 13.9 - - - +
27A VAL 3.6 10.7 + - - -
29A ILE* 3.8 4.5 - - - -
88A GLY* 1.3 75.4 - - - -
90A GLY* 1.3 62.1 + - - +
102A THR* 2.8 22.2 + - - -
103A ASN* 4.7 3.0 + - - +
106A VAL* 5.5 0.8 - - - +
167A ILE 4.0 0.3 + - - -
168A GLY* 3.8 15.4 - - - -
169A ASN* 3.7 24.9 - - - +
175A GLU* 5.5 0.7 + - - -
211A GLY 5.2 0.2 - - - -
212A GLY* 3.9 25.1 + - - +
213A ALA 4.9 0.3 + - - -
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Residues in contact with GLY 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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26A VAL* 3.4 11.8 - - - +
27A VAL* 2.9 42.8 + - - +
29A ILE* 4.4 1.1 - - - -
89A SER* 1.3 77.1 + - - +
91A VAL* 1.3 65.7 + - - +
100A VAL* 4.1 4.3 - - - -
101A VAL 3.3 12.3 - - - -
102A THR* 4.3 2.2 - - - -
212A GLY* 5.6 1.3 - - - -
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Residues in contact with VAL 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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25A SER* 3.4 11.7 - - - +
26A VAL* 5.0 3.6 - - + +
90A GLY* 1.3 80.0 - - - +
92A ILE* 1.3 65.7 + - - +
93A ILE 3.2 0.9 + - - -
100A VAL* 3.3 5.0 - - - +
101A VAL* 2.8 45.6 + - + +
150A ILE* 3.4 42.2 - - + -
212A GLY 4.9 0.7 - - - -
213A ALA* 3.6 32.8 - - + +
221A LEU* 4.4 4.5 - - + -
224A ILE* 3.9 18.8 - - + -
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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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24A PRO 4.0 9.9 - - - +
25A SER 2.7 10.9 + - - +
27A VAL* 3.6 30.3 - - + +
90A GLY 4.4 0.2 - - - -
91A VAL* 1.3 69.3 - - - +
93A ILE* 1.3 60.0 + - - +
94A ASP 3.9 21.1 - - - +
95A ALA* 4.1 4.7 - - - +
99A TYR 3.6 5.8 - - - +
100A VAL* 3.8 12.6 - - + -
117A LEU* 4.0 8.7 - - + -
141A ILE* 4.6 0.7 - - + -
147A LEU* 3.6 30.5 - - + -
148A THR 3.3 28.3 - - - +
149A ALA* 3.3 7.7 - - - -
150A ILE* 3.0 29.8 + - - +
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Residues in contact with ILE 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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91A VAL 3.2 5.3 + - - +
92A ILE* 1.3 73.1 - - - +
94A ASP* 1.3 57.7 + - + +
99A TYR* 2.6 37.7 + - + +
101A VAL* 4.2 17.7 - - + +
138A LEU* 4.6 11.2 - - + -
149A ALA* 3.9 10.4 - - - +
150A ILE* 3.5 30.1 - - + +
152A MET* 3.3 48.2 - - + +
221A LEU* 4.0 9.0 - - + -
247A VAL* 5.8 2.5 - - + -
251A THR* 5.4 9.4 - - - +
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Residues in contact with ASP 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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92A ILE* 3.6 4.4 - - - +
93A ILE* 1.3 81.5 - - + +
95A ALA* 1.3 54.7 + - - +
96A ASP* 3.0 8.5 + - - +
97A LYS* 2.6 49.1 + - - +
98A GLY* 2.7 29.8 + - - -
99A TYR* 2.9 38.8 + - + -
149A ALA* 4.3 1.3 - - - -
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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