Contacts of the strand formed by residues 124 - 129 (chain A) in PDB entry 4MDH
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ASP 3.2 13.3 + - - +
82A VAL* 3.5 3.8 - - + -
83A ALA 3.2 20.7 + - - -
122A SER 3.6 15.9 - - - +
123A VAL* 1.3 73.7 - - - +
125A VAL* 1.4 59.9 - - - +
126A ILE* 3.4 16.1 - - + +
149A GLU* 5.5 2.4 + - - +
150A ASN* 3.4 32.0 + - + +
256A ILE* 5.1 11.0 - - + -
257A TRP* 4.7 16.2 - - + -
294A LYS* 3.1 46.1 + - - +
295A THR* 5.1 5.3 + - - +
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Residues in contact with VAL 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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83A ALA* 3.8 7.9 - - + +
85A LEU* 4.3 18.8 - - + -
115A LEU* 3.9 25.4 - - + -
123A VAL* 4.1 13.0 - - + +
124A LYS* 1.4 71.8 - - - +
126A ILE* 1.4 59.6 + - - +
127A VAL* 3.8 16.4 - - + -
139A ALA* 5.6 0.4 - - + -
146A ILE* 5.2 0.2 - - + -
150A ASN 3.1 10.4 + - - +
151A PHE* 3.3 49.4 - - + -
152A SER* 3.3 27.0 + - - +
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Residues in contact with ILE 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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82A VAL* 3.9 16.4 - - + -
83A ALA 2.9 16.6 + - - +
84A ILE* 3.4 12.2 - - + +
85A LEU* 2.6 33.4 + - - +
124A LYS* 3.4 24.7 - - + +
125A VAL* 1.4 71.3 - - - +
127A VAL* 1.3 59.9 + - - +
128A VAL* 4.0 15.6 + - + -
152A SER* 3.7 3.6 - - - +
154A LEU* 4.9 4.9 - - + -
249A ILE* 4.9 1.3 - - + -
252A HIS* 3.8 43.1 - - + +
253A VAL* 4.2 21.1 - - + -
256A ILE* 4.6 8.3 - - + -
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Residues in contact with VAL 127 (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 LEU* 4.2 5.8 - - + -
108A PHE* 3.4 37.9 - - + -
125A VAL* 3.8 20.0 - - + -
126A ILE* 1.3 75.8 - - - +
128A VAL* 1.3 62.1 + - - +
129A GLY 4.4 2.7 - - - +
132A ALA* 4.0 8.3 - - - +
135A ASN* 4.2 3.1 - - + -
136A CYS* 3.6 49.4 - - + +
139A ALA* 5.2 2.5 - - + -
151A PHE* 4.8 1.1 - - + -
152A SER 3.2 7.2 + - - +
153A CYS* 3.4 2.8 - - + +
154A LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 128 (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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15A ILE* 4.5 8.7 - - + -
84A ILE* 4.6 8.1 - - + -
85A LEU 3.2 9.9 + - - +
86A VAL* 4.1 9.4 - - + -
126A ILE* 4.4 15.0 - - + +
127A VAL* 1.3 76.3 - - - +
129A GLY* 1.3 70.5 + - - +
130A ASN* 3.2 1.2 + - - +
132A ALA* 3.6 3.3 - - - +
154A LEU* 4.3 13.5 - - + -
245A ALA* 5.5 0.4 - - + -
249A ILE* 3.9 36.1 - - + -
335A NAD 3.1 57.8 + - + +
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Residues in contact with GLY 129 (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 LEU 3.1 10.1 + - - -
86A VAL 3.7 6.8 + - - -
88A SER* 3.2 24.0 - - - -
108A PHE* 3.9 7.3 - - - -
127A VAL* 4.4 1.6 - - - +
128A VAL* 1.3 75.3 - - - +
130A ASN* 1.3 54.8 + - - -
131A PRO 3.7 5.4 - - - -
132A ALA* 3.7 4.2 - - - +
135A ASN* 2.5 30.8 + - - +
335A NAD 3.5 6.7 - - - -
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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