Contacts of the strand formed by residues 34 - 38 (chain i) in PDB entry 5GJQ
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 SER 34 (chain i).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32i ALA 3.8 0.3 + - - -
33i PRO* 1.3 74.4 + - - +
35i VAL* 1.3 61.4 + - - +
46i ALA 3.2 12.1 - - - -
47i THR* 2.8 23.6 + - - -
74i VAL* 4.9 5.2 - - - -
75i TYR 3.0 21.2 + - - -
76i SER* 3.3 9.6 + - - -
134i LEU* 4.5 10.0 - - - +
161i ALA* 3.1 6.3 - - - +
162i MET* 2.9 38.9 + - - +
194i LEU* 4.7 2.9 - - - -
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Residues in contact with VAL 35 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34i SER* 1.3 77.0 - - - +
36i GLY* 1.3 58.5 + - - +
37i ILE* 5.2 2.0 - - + -
44i VAL 3.9 0.9 - - - +
45i LEU* 3.5 2.3 - - - -
46i ALA* 2.9 35.4 + - + +
134i LEU* 4.1 6.1 - - - +
160i THR 3.5 8.1 - - - +
161i ALA* 4.8 5.8 - - + -
173i LEU* 5.0 2.7 - - + -
190i ALA* 4.4 12.9 - - + +
193i THR* 3.7 29.8 - - + +
194i LEU* 5.0 6.0 - - + +
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Residues in contact with GLY 36 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35i VAL* 1.3 74.8 - - - +
37i ILE* 1.4 63.4 + - - +
44i VAL 3.3 8.3 - - - -
45i LEU* 3.9 13.5 - - - -
134i LEU* 4.0 6.3 - - - +
145i LEU* 3.4 13.8 - - - +
159i ALA* 3.1 4.7 - - - -
160i THR 2.9 35.2 + - - +
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Residues in contact with ILE 37 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35i VAL* 5.2 0.7 - - + -
36i GLY* 1.4 79.8 - - - +
38i LYS* 1.3 74.2 + - - +
39i ALA* 3.8 1.7 + - - +
43i VAL* 3.4 6.0 - - - +
44i VAL* 2.9 41.1 + - + +
145i LEU* 4.0 0.8 - - - +
158i LYS 3.8 5.4 - - - +
159i ALA* 4.2 12.6 - - + -
173i LEU* 4.1 13.7 - - + -
177i TYR* 5.3 4.9 - - + -
181i LEU* 4.6 12.6 - - + -
186i ALA* 3.5 37.0 - - + +
189i THR* 3.5 20.6 - - + +
190i ALA* 3.7 20.9 - - + +
193i THR* 4.9 0.4 - - + -
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Residues in contact with LYS 38 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37i ILE* 1.3 78.9 - - - +
39i ALA* 1.3 61.6 + - - +
40i ALA* 4.1 7.4 + - - +
42i GLY 3.7 3.4 - - - -
43i VAL* 4.1 5.1 - - + +
142i ARG* 6.0 0.2 - - - -
143i PRO* 3.7 47.3 - - + +
145i LEU* 4.0 20.8 - - + +
157i TRP 4.3 6.7 - - - +
158i LYS* 2.8 35.9 + - + +
178i ASN 5.5 2.9 - - - +
179i GLU* 5.8 5.1 - - - +
181i LEU* 5.7 0.3 - - - +
57j ASP* 3.1 39.8 + - - +
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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