Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 3MX0
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 ASN 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A THR* 4.3 1.7 + - - +
119A PHE* 1.3 109.3 - - - +
121A LEU* 1.3 60.0 + - - +
122A TYR* 3.2 24.4 + - + -
141A LYS* 2.9 29.5 - - - +
143A ASP 4.1 2.2 - - - -
144A THR* 3.1 12.2 - - - +
182A PHE* 3.0 12.6 - - - +
183A GLN* 2.8 52.1 + - + -
185A ILE* 5.0 9.5 - - - +
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Residues in contact with LEU 121 (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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96A ILE* 4.3 19.7 - - + -
98A LEU* 3.7 23.6 - - + -
119A PHE* 4.3 0.9 + - + -
120A ASN* 1.3 70.5 - - - +
122A TYR* 1.3 77.6 + - - +
141A LYS* 3.5 4.0 - - - +
142A ILE* 3.2 37.7 + - + -
143A ASP 3.3 9.4 + - - +
145A ILE* 3.8 28.8 - - + +
168A ARG* 4.7 9.4 - - + -
180A LEU* 4.9 7.2 - - + -
181A ALA 4.2 1.8 - - - +
182A PHE* 3.3 39.9 - - + -
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Residues in contact with TYR 122 (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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80A TRP* 3.1 37.4 - + + -
120A ASN* 3.2 37.2 + - + -
121A LEU* 1.3 95.7 - - - +
123A TYR* 1.3 69.5 + - - +
136A LYS 5.7 0.2 - - - -
139A PHE* 3.5 29.4 - - + -
140A THR 3.4 19.5 - - - -
141A LYS* 3.7 21.1 - - + +
142A ILE* 4.0 6.3 - - - +
180A LEU* 3.2 22.2 - - - +
181A ALA 2.9 17.9 + - - +
183A GLN* 3.0 21.5 + - + -
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Residues in contact with TYR 123 (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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94A ILE* 6.1 2.7 - - + -
122A TYR* 1.3 83.7 - - - +
124A ALA* 1.3 65.6 + - - +
125A GLU* 3.8 30.0 - - + +
138A LEU 4.3 0.5 - - - +
139A PHE* 3.5 8.9 - - - -
140A THR* 3.1 53.7 + - - -
141A LYS 5.7 1.1 - - - -
142A ILE* 4.1 24.2 - - + -
170A VAL* 4.2 27.5 - - + +
171A GLY 5.6 2.1 + - - -
172A PRO 5.5 1.9 + - - -
173A LEU* 4.2 16.2 - - + +
178A PHE* 5.3 3.6 - - + -
179A TYR 3.0 11.4 - - - +
180A LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 124 (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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123A TYR* 1.3 76.8 - - - +
125A GLU* 1.3 67.7 + - - +
126A SER* 3.5 0.4 + - - -
138A LEU* 4.3 13.5 - - + +
139A PHE* 3.7 22.9 - - + -
178A PHE* 2.8 9.8 - - - -
179A TYR* 2.8 57.8 + - + -
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Residues in contact with GLU 125 (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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88A ARG* 5.2 0.2 - - - -
123A TYR* 3.8 25.9 - - + +
124A ALA* 1.3 76.5 - - - +
126A SER* 1.3 59.6 - - - +
130A TYR* 5.9 0.3 - - - -
138A LEU* 5.5 6.1 - - - +
172A PRO 4.0 1.7 - - - +
173A LEU* 3.1 23.9 - - + +
174A THR* 2.9 48.7 + - - +
175A ARG* 3.6 32.8 + - + +
177A GLY 3.7 3.6 - - - -
178A PHE* 4.3 2.5 - - + +
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Residues in contact with SER 126 (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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85A TRP* 3.2 17.4 + - - -
124A ALA* 3.5 0.6 + - - -
125A GLU* 1.3 74.3 - - - +
127A ASP* 1.3 65.0 + - - +
128A LEU* 2.7 32.1 + - - +
130A TYR* 4.4 16.6 - - - -
175A ARG* 4.0 2.4 - - - +
176A LYS* 3.7 2.8 + - - +
177A GLY 2.5 40.3 + - - +
179A TYR* 4.0 16.6 - - - -
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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