Contacts of the helix formed by residues 56 - 67 (chain A) in PDB entry 3SRF
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A PRO 5.3 0.6 + - - -
54A SER 3.4 0.2 - - - -
55A ARG* 1.3 81.0 - - - +
57A VAL* 1.3 58.9 + - - +
58A GLU* 3.7 17.8 + - - +
59A THR* 2.7 32.2 + - - -
60A LEU* 3.0 26.1 + - - +
89A ASN* 3.8 5.2 - - - +
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Residues in contact with VAL 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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55A ARG 3.8 0.4 + - - -
56A SER* 1.3 71.3 - - - +
58A GLU* 1.3 69.0 + - - +
60A LEU* 3.0 9.2 + - - +
61A LYS* 2.8 48.6 + - - +
89A ASN* 3.6 34.5 - - + +
92A THR* 4.4 15.5 - - + -
93A ALA* 3.9 24.0 - - + +
517D GLY* 6.2 5.4 - - - -
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Residues in contact with GLU 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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56A SER* 3.3 18.2 + - - +
57A VAL* 1.3 86.0 + - - +
59A THR* 1.3 61.1 + - - +
61A LYS* 3.8 12.2 + - + +
62A GLU* 3.4 25.8 + - - +
517D GLY* 5.4 9.7 - - - +
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Residues in contact with THR 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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53A ALA 4.0 21.0 + - - +
54A SER* 4.0 14.5 - - - -
56A SER* 2.7 26.5 + - - -
57A VAL 3.2 0.4 - - - -
58A GLU* 1.3 76.8 - - - +
60A LEU* 1.3 60.8 + - - +
62A GLU* 3.2 6.8 + - + +
63A MET* 2.8 42.1 + - + +
370A PRO* 5.2 5.4 - - + -
371A LEU* 5.0 11.2 - - + -
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Residues in contact with LEU 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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50A ILE* 3.8 28.5 - - + -
54A SER 3.4 20.2 - - - +
55A ARG* 3.5 21.5 - - - +
56A SER 3.0 10.7 + - - +
57A VAL* 3.0 4.0 + - - +
59A THR* 1.3 74.5 - - - +
61A LYS* 1.3 60.4 + - - +
63A MET* 3.7 7.7 - - - +
64A ILE* 3.0 36.5 + - + +
68A MET* 4.1 16.3 - - + +
86A THR 4.7 0.2 - - - +
89A ASN* 3.7 8.7 - - + +
90A VAL* 3.5 39.3 - - + +
93A ALA* 3.9 11.2 - - + -
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Residues in contact with LYS 61 (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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57A VAL* 2.8 36.1 + - + +
58A GLU* 3.8 12.8 - - - +
60A LEU* 1.3 77.5 - - - +
62A GLU* 1.3 62.7 + - + +
64A ILE* 3.6 2.9 + - - +
65A LYS* 3.2 30.5 + - + +
92A THR* 6.2 0.7 - - - -
93A ALA* 3.8 11.0 - - + +
96A SER* 3.5 35.2 - - - +
97A PHE* 3.9 15.1 - - + -
517D GLY 4.8 11.3 + - - -
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Residues in contact with GLU 62 (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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58A GLU 3.4 15.0 - - - +
59A THR* 3.2 10.4 + - - +
61A LYS* 1.3 79.6 - - + +
63A MET* 1.3 58.8 + - - +
65A LYS* 3.5 24.7 + - - +
66A SER* 2.9 30.7 + - - -
371A LEU* 3.7 24.5 - - + -
375A ARG* 4.6 9.2 + - - -
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Residues in contact with MET 63 (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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48A CYS* 3.7 37.7 - - + -
50A ILE* 4.9 2.5 - - + -
54A SER* 3.6 28.3 - - - -
59A THR* 2.8 23.6 + - + +
60A LEU* 3.7 17.5 - - - +
61A LYS 3.3 0.2 - - - -
62A GLU* 1.3 75.4 - - - +
64A ILE* 1.3 64.3 + - - +
66A SER* 3.1 5.5 + - - -
67A GLY 3.0 19.1 + - - -
68A MET* 3.0 19.7 + - + +
364A THR* 3.8 21.3 - - + -
370A PRO* 4.6 7.6 - - + +
371A LEU* 3.8 17.9 - - + -
374A VAL* 3.8 10.3 - - + +
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Residues in contact with ILE 64 (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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60A LEU* 3.0 23.2 + - + +
61A LYS 3.9 4.0 - - - +
63A MET* 1.3 74.8 - - - +
65A LYS* 1.3 62.0 + - - +
67A GLY* 3.2 15.1 + - - -
68A MET* 3.5 31.1 + - + +
90A VAL* 4.7 1.6 - - + +
93A ALA* 3.7 30.5 - - + +
94A THR* 3.8 22.2 - - - +
97A PHE* 4.5 16.2 - - + -
105A ARG* 4.1 31.0 - - + +
107A VAL* 4.1 19.5 - - + -
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Residues in contact with LYS 65 (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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61A LYS* 3.2 17.8 + - + +
62A GLU* 3.6 28.7 + - - +
63A MET 3.2 0.4 - - - -
64A ILE* 1.3 75.1 - - - +
66A SER* 1.3 62.5 + - - +
67A GLY* 4.6 0.2 - - - -
97A PHE* 3.6 29.2 - - + -
105A ARG* 4.0 21.8 + - - +
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Residues in contact with SER 66 (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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62A GLU 2.9 19.8 + - - -
63A MET* 3.1 12.1 + - - -
65A LYS* 1.3 79.2 - - - +
67A GLY* 1.3 56.1 + - - +
371A LEU* 3.5 12.9 + - - +
374A VAL* 3.7 23.2 - - - +
375A ARG* 3.1 41.2 + - - +
378A HIS* 4.2 18.9 + - - +
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Residues in contact with GLY 67 (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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42A ARG* 2.8 30.9 + - - -
46A ILE* 3.6 4.0 - - - +
63A MET 3.0 2.0 + - - -
64A ILE 3.2 8.9 + - - -
65A LYS 4.5 0.4 - - - -
66A SER* 1.3 79.9 - - - +
68A MET* 1.3 68.3 + - - +
69A ASN* 3.2 12.6 + - - +
105A ARG* 5.6 4.7 - - - -
374A VAL* 3.6 8.7 - - - +
378A HIS* 5.2 0.4 - - - -
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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