Contacts of the helix formed by residues 168 - 177 (chain n) 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 ALA 168 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35n THR* 3.0 25.6 + - - +
167n LYS* 1.3 73.3 - - + +
169n ARG* 1.3 62.3 + - - +
170n GLN 3.7 1.1 - - - -
171n ALA* 4.3 9.4 - - + +
172n ALA* 3.1 22.6 + - - +
200n VAL* 3.5 35.9 - - + +
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Residues in contact with ARG 169 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379L LYS* 5.0 11.7 - - - +
31n GLU* 6.4 0.6 - - - +
164n ALA* 3.0 37.0 - - + +
165n ILE* 3.9 9.9 - - + +
166n GLY 3.5 12.2 + - - +
167n LYS 3.1 6.7 + - - +
168n ALA* 1.3 73.2 - - - +
170n GLN* 1.3 96.1 + - + +
172n ALA* 3.3 4.7 + - - +
173n LYS* 2.9 46.1 + - - +
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Residues in contact with GLN 170 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334L LEU* 5.9 1.2 - - - +
372L ARG* 4.1 39.4 + - + +
376L ASP* 5.2 15.0 + - - +
167n LYS 5.1 0.2 + - - -
168n ALA* 4.7 0.2 - - - +
169n ARG* 1.3 101.4 + - + +
171n ALA* 1.3 67.8 + - - +
173n LYS* 2.9 36.5 + - - +
174n THR* 2.9 15.1 + - - -
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Residues in contact with ALA 171 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168n ALA* 4.3 12.2 - - + -
169n ARG 3.3 0.4 - - - -
170n GLN* 1.3 77.7 - - - +
172n ALA* 1.3 65.1 + - - +
174n THR* 3.1 14.6 + - - +
175n GLU* 3.0 23.6 + - + +
200n VAL* 3.7 18.8 - - + -
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Residues in contact with ALA 172 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35n THR* 4.8 0.2 - - + -
37n ILE* 4.1 13.7 - - + -
164n ALA* 3.7 19.1 - - + -
168n ALA 3.1 19.5 + - - +
169n ARG 3.3 3.8 + - - +
170n GLN 3.2 0.4 - - - -
171n ALA* 1.3 80.7 - - - +
173n LYS* 1.3 56.1 + - - +
175n GLU* 3.1 4.0 + - - +
176n ILE* 2.9 34.2 + - + +
196n ILE* 4.2 10.5 - - + -
200n VAL* 3.5 15.2 - - + +
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Residues in contact with LYS 173 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334L LEU* 5.5 3.4 - - - +
372L ARG* 4.0 22.0 - - - +
58h ASP* 2.9 32.0 + - - +
60h LEU* 3.9 17.9 - - + +
160n TYR* 5.8 9.1 - - + -
163n CYS* 5.8 2.5 - - - -
164n ALA* 5.0 12.1 - - + +
169n ARG* 2.9 42.1 + - - +
170n GLN* 2.9 26.5 + - - +
172n ALA* 1.3 75.2 - - - +
174n THR* 1.3 62.8 + - - +
176n ILE* 3.1 5.3 + - + +
177n GLU* 3.0 29.9 + - + +
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Residues in contact with THR 174 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365L GLU* 5.7 0.8 + - + -
368L MET* 4.2 13.7 - - - +
369L LYS* 4.6 23.9 + - + +
372L ARG* 3.5 21.1 + - - +
170n GLN 2.9 11.3 + - - -
171n ALA* 3.4 14.4 - - - +
173n LYS* 1.3 77.8 - - - +
175n GLU* 1.3 79.8 + - + +
176n ILE 3.4 0.5 + - - -
177n GLU* 3.6 14.0 + - - +
178n LYS* 3.7 22.8 - - - +
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Residues in contact with GLU 175 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369L LYS* 6.1 0.7 - - - -
171n ALA* 3.0 14.8 + - + +
172n ALA* 3.1 8.5 + - - +
174n THR* 1.3 89.7 - - + +
176n ILE* 1.3 60.3 + - - +
178n LYS* 3.5 45.7 + - - +
179n LEU* 4.5 3.6 + - - +
195n LYS* 5.5 1.7 + - - -
196n ILE* 3.8 29.9 - - + +
199n ILE* 3.2 46.7 - - + +
200n VAL* 5.3 0.9 - - + -
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Residues in contact with ILE 176 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60h LEU* 3.8 24.9 - - + +
37n ILE* 4.7 10.3 - - + -
38n GLY 5.1 1.6 - - - +
39n ILE* 5.0 14.8 - - + -
162n GLY* 4.3 12.8 - - - -
163n CYS* 4.0 31.9 - - - +
164n ALA* 4.6 3.8 - - + -
172n ALA* 2.9 27.3 + - + +
173n LYS* 3.1 8.7 + - - +
175n GLU* 1.3 74.0 - - - +
177n GLU* 1.3 57.5 + - - +
178n LYS 3.0 4.9 - - - -
179n LEU* 2.9 30.3 + - + +
181n MET* 4.6 6.3 - - + +
196n ILE* 3.4 23.1 - - + -
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Residues in contact with GLU 177 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334L LEU* 4.5 6.8 - - - +
364L GLN* 5.8 0.2 - - - +
368L MET* 4.8 12.8 - - - +
372L ARG* 3.3 34.2 + - - -
58h ASP* 3.5 17.3 - - - +
59h LYS* 2.6 51.9 + - - +
60h LEU* 4.0 14.8 - - + -
173n LYS 3.0 16.4 + - - +
174n THR* 3.9 11.1 + - - +
175n GLU 3.4 0.2 - - - -
176n ILE* 1.3 74.1 - - - +
178n LYS* 1.3 58.1 + - + +
179n LEU 3.2 3.8 + - - +
180n GLN* 4.8 3.1 + - - -
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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