Contacts of the strand formed by residues 121 - 125 (chain A) in PDB entry 1EAN
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 THR 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.4 21.3 - - + -
103A VAL 3.3 9.9 - - - +
104A THR* 3.7 17.1 - - + +
119A ASN* 3.3 5.9 - - - +
120A ALA* 1.3 81.7 + - - +
122A ALA* 1.3 71.6 + - - +
131A PHE* 3.8 6.1 - - - -
132A ASN 5.8 0.3 + - - -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.5 5.9 - - - +
103A VAL* 2.9 31.0 + - - +
121A THR* 1.3 78.2 - - - +
123A ALA* 1.3 61.8 + - - +
129A ALA* 4.1 8.3 - - + -
130A ARG 3.6 25.4 - - - +
131A PHE* 3.8 30.0 - - + +
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Residues in contact with ALA 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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100A GLY* 4.3 19.1 - - - +
101A THR 3.4 7.9 - - - +
102A LEU* 4.3 9.2 - - + -
122A ALA* 1.3 76.7 - - - +
124A MET* 1.3 65.7 + - - +
125A LYS* 3.6 3.5 + - - +
128A VAL 3.7 1.0 - - - +
129A ALA* 3.5 16.1 - - - -
130A ARG 4.3 2.8 + - - +
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Residues in contact with MET 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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70A PHE* 4.6 7.2 - - + -
91A VAL* 3.7 27.8 - - + +
93A ALA* 3.9 24.2 - - + +
97A VAL* 3.8 20.2 - - + +
98A PRO 3.7 17.5 - - - +
99A ASP* 3.4 3.1 - - - +
100A GLY* 2.8 26.5 + - - -
101A THR* 2.8 21.3 + - - +
103A VAL* 4.0 21.3 - - + -
123A ALA* 1.3 74.4 - - - +
125A LYS* 1.3 59.7 + - - +
127A GLN* 3.4 32.1 - - - +
128A VAL 3.5 4.0 - - - +
129A ALA* 3.7 5.4 - - + -
152A VAL* 4.9 1.3 - - + -
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Residues in contact with LYS 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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99A ASP* 3.4 29.5 + - + +
123A ALA 4.7 2.5 - - - +
124A MET* 1.3 76.0 - - - +
126A ASN* 1.3 92.1 + - - +
128A VAL* 2.9 24.2 + - - +
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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