Contacts of the strand formed by residues 126 - 129 (chain B) in PDB entry 3EGC
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 GLY 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B VAL 4.2 0.8 + - - -
70B VAL* 3.5 4.1 - - - +
71B GLY 2.9 23.9 + - - -
124B VAL* 3.2 5.1 + - - +
125B ASP* 1.3 78.9 - - - +
127B LEU* 1.3 65.2 + - - +
147B PHE* 4.0 6.7 - - - -
148B PRO* 3.4 15.0 - - - -
311B LEU* 3.7 18.6 - - - -
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Residues in contact with LEU 127 (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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71B GLY* 3.2 21.5 - - - +
73B ILE* 4.3 7.2 - - + -
116B VAL* 4.0 37.7 - - + +
119B PHE* 3.9 17.5 - - + -
124B VAL* 3.8 14.4 - - + -
126B GLY* 1.3 79.8 - - - +
128B ILE* 1.4 65.4 + - - +
129B LEU* 4.1 5.6 + - + +
139B LEU* 5.2 0.4 - - + -
147B PHE* 3.5 23.6 - - + -
148B PRO 3.1 6.3 + - - -
149B ILE* 3.5 24.7 - - + -
150B VAL 3.0 25.3 + - - +
311B LEU* 3.6 6.2 - - - +
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Residues in contact with ILE 128 (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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70B VAL* 4.5 1.3 - - + -
71B GLY 2.8 10.0 + - - +
72B LEU* 3.4 24.2 - - + +
73B ILE* 2.9 28.6 + - - +
85B VAL* 5.8 0.2 - - + -
89B VAL* 3.8 17.9 - - + -
127B LEU* 1.4 71.6 - - - +
129B LEU* 1.3 62.4 + - - +
130B ALA 4.1 0.2 - - - -
150B VAL* 3.3 9.6 - - + +
152B VAL* 4.0 26.0 - - + -
307B ALA* 3.6 10.5 - - + -
308B MET* 3.4 48.0 - - + +
311B LEU* 3.8 20.4 - - + +
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Residues in contact with LEU 129 (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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73B ILE* 3.5 30.7 - - + +
112B GLU* 3.5 40.6 - - + +
116B VAL* 5.1 2.9 - - + -
127B LEU* 3.9 8.5 - - + -
128B ILE* 1.3 74.9 - - - +
130B ALA* 1.3 62.9 + - - +
131B PRO* 3.3 11.0 - - + +
138B TYR* 5.1 0.2 - - - +
139B LEU* 4.1 27.1 - - + -
149B ILE* 4.6 11.7 - - + -
150B VAL 2.9 11.8 + - - +
151B ALA* 3.1 7.4 - - - -
152B VAL* 2.9 25.8 + - - -
156B LEU* 4.1 20.0 - - + -
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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