Contacts of the helix formed by residues 50 - 60 (chain A) in PDB entry 2GTI
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 PRO 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PRO 4.6 1.3 - - - +
49A PHE* 1.3 91.9 - - + +
51A THR* 1.3 61.0 + - - +
52A ASN* 3.7 15.7 - - - +
53A VAL* 3.0 16.3 + - + +
54A ALA 2.8 24.8 + - - -
104A TYR* 4.2 25.8 - - + +
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Residues in contact with THR 51 (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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26A VAL* 3.7 19.3 - - + -
28A GLY 2.6 27.2 + - - +
29A GLU* 3.3 24.5 - - - +
30A LYS 4.0 0.9 - - - +
31A VAL* 3.5 24.5 - - + -
43A PHE* 4.3 1.0 - - + -
45A ASN* 3.4 18.9 + - + +
49A PHE 3.4 2.0 + - - -
50A PRO* 1.3 71.1 - - - +
52A ASN* 1.3 63.3 + - - +
54A ALA* 3.1 3.3 + - - +
55A VAL* 3.1 22.9 + - - +
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Residues in contact with ASN 52 (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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2A LEU* 4.0 27.0 - - + +
26A VAL* 4.3 16.7 - - + +
31A VAL* 5.2 0.2 - - - -
50A PRO* 3.7 16.3 - - - +
51A THR* 1.3 77.0 + - - +
53A VAL* 1.3 74.1 + - - +
55A VAL* 3.2 25.3 - - - +
56A GLU* 3.6 8.7 + - - +
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Residues in contact with VAL 53 (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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49A PHE* 4.2 10.8 - - + -
50A PRO* 3.0 19.4 + - + +
52A ASN* 1.3 95.2 - - - +
54A ALA* 1.3 63.8 + - - +
56A GLU* 3.2 9.9 + - - +
57A LEU* 3.1 25.8 + - + +
102A CYS* 4.2 9.2 - - - -
104A TYR* 3.7 32.5 - - + -
105A THR* 3.5 30.3 - - + -
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Residues in contact with ALA 54 (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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43A PHE* 3.7 11.3 - - + -
45A ASN* 3.3 29.8 - - - +
47A THR* 3.4 15.0 - - + +
49A PHE* 4.3 5.4 - - + -
50A PRO 2.8 11.3 + - - +
51A THR 3.1 8.9 + - - +
53A VAL* 1.3 78.0 - - - +
55A VAL* 1.3 57.3 + - - +
57A LEU* 3.3 9.0 + - - +
58A PHE* 3.0 28.2 + - - +
86A TRP* 4.6 3.0 - - - -
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Residues in contact with VAL 55 (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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2A LEU* 3.9 20.9 - - + -
5A VAL* 3.8 12.3 - - + +
6A VAL* 4.8 7.9 - - + -
9A LEU* 3.8 25.8 - - + -
31A VAL* 4.0 11.0 - - + -
42A VAL* 5.5 0.2 - - + -
43A PHE* 3.7 35.8 - - + -
51A THR 3.1 9.6 + - - +
52A ASN* 3.2 20.0 - - - +
54A ALA* 1.3 73.6 - - - +
56A GLU* 1.3 60.6 + - - +
58A PHE* 3.9 0.5 - - - +
59A ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 56 (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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0A SER* 3.4 23.9 + - - +
5A VAL* 3.7 28.9 - - + -
52A ASN 4.0 8.9 - - - +
53A VAL* 3.2 12.6 + - - +
54A ALA 3.2 0.4 - - - -
55A VAL* 1.3 83.8 - - - +
57A LEU* 1.3 57.6 + - - +
59A ALA* 3.4 2.3 + - - +
60A LYS* 2.7 56.7 + - + +
102A CYS* 3.5 34.1 - - + +
103A LYS* 4.6 2.4 + - - +
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Residues in contact with LEU 57 (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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49A PHE* 3.5 45.8 - - + -
53A VAL* 3.1 26.5 + - + +
54A ALA* 3.7 7.0 - - - +
55A VAL 3.3 0.4 - - - -
56A GLU* 1.3 75.3 - - - +
58A PHE* 1.3 64.0 + - - +
60A LYS* 3.3 3.6 + - - +
61A ARG* 3.2 17.3 + - - +
84A VAL* 3.6 18.1 - - + +
86A TRP* 4.7 2.7 - - - -
93A VAL* 3.9 16.4 - - + -
98A THR* 3.7 27.4 - - + -
101A VAL* 4.5 9.0 - - + -
102A CYS* 3.9 22.4 - - + -
105A THR* 4.1 3.1 - - + +
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Residues in contact with PHE 58 (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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9A LEU* 3.7 31.0 - - + -
42A VAL 5.7 0.7 - - - -
43A PHE* 3.7 26.7 - + + -
54A ALA 3.0 16.9 + - - +
55A VAL 3.9 2.0 - - - +
57A LEU* 1.3 76.1 - - - +
59A ALA* 1.3 62.3 + - - +
61A ARG* 2.9 73.6 + - - +
86A TRP* 3.7 41.5 - + + -
88A TYR* 4.6 7.0 - + - -
601A GOL 3.8 27.8 - - - -
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Residues in contact with ALA 59 (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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5A VAL* 3.9 22.2 - - + +
9A LEU* 3.9 26.0 - - + -
14A HIS* 3.3 11.7 + - - +
15A PHE* 2.7 37.3 + - + +
55A VAL 2.9 19.6 + - - +
56A GLU 3.7 4.5 - - - +
57A LEU 3.3 0.2 - - - -
58A PHE* 1.3 77.0 - - - +
60A LYS* 1.3 57.8 + - - +
61A ARG* 3.2 1.6 + - - +
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Residues in contact with LYS 60 (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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0A SER* 3.1 23.9 + - - +
15A PHE* 3.9 38.6 - - + -
56A GLU* 2.7 48.5 + - + +
57A LEU* 4.0 4.5 - - - +
58A PHE 3.1 0.4 - - - -
59A ALA* 1.3 74.7 - - + +
61A ARG* 1.3 67.9 + - - +
62A SER* 3.6 0.5 + - - -
83A HIS* 5.7 0.5 - - - -
84A VAL* 3.1 20.0 + - + +
101A VAL* 3.0 36.3 + - + +
102A CYS* 5.5 0.2 - - + -
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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