Contacts of the helix formed by residues 57 - 75 (chain A) in PDB entry 5GQQ
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 ASP 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A SER* 2.9 13.5 + - - +
56A MET* 1.3 80.4 - - - +
58A TRP* 1.3 63.2 + - - +
59A ASP* 3.3 15.4 + - - +
60A SER* 3.0 32.3 + - - -
61A ALA* 2.9 19.0 + - - +
37C LYS* 6.4 1.8 - - - -
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Residues in contact with TRP 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 MET 3.8 3.4 + - - -
57A ASP* 1.3 72.9 + - - +
59A ASP* 1.3 91.4 + - - +
61A ALA* 3.9 0.3 - - - +
62A ILE* 2.9 56.9 + - + +
91A SER* 2.9 24.0 + - - -
93A VAL* 4.0 13.9 - - + -
105A ILE* 3.8 31.2 - - + +
146A SER* 3.7 20.9 - - - -
147A SER* 3.8 11.7 - - - -
148A ALA* 3.8 26.3 - - + +
151A ASN* 3.5 25.8 - - - -
174A TYR* 5.1 3.6 - - - +
176A THR* 3.7 18.5 + - + +
182A PRO* 5.1 4.9 - - + -
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 3.0 11.8 + - - +
58A TRP* 1.3 87.7 - - - +
60A SER* 1.3 61.2 + - - +
62A ILE* 3.3 18.7 - - - +
63A GLN* 3.5 7.3 + - - +
146A SER 4.4 1.0 - - - +
147A SER* 3.2 15.0 - - - -
148A ALA* 3.1 35.1 + - - +
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Residues in contact with SER 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 5.2 1.3 - - - -
57A ASP* 3.0 31.6 + - - -
59A ASP* 1.3 76.7 - - - +
61A ALA* 1.3 54.4 + - - +
63A GLN* 3.0 23.6 + - - +
64A THR* 2.8 42.2 + - - -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 3.6 29.8 - - + +
55A SER* 4.1 4.7 - - - -
57A ASP 2.9 15.2 + - - +
58A TRP 3.9 0.4 - - - +
60A SER* 1.3 76.4 - - - +
62A ILE* 1.3 53.6 + - - +
64A THR* 3.5 7.9 - - - -
65A GLY* 2.6 35.7 + - - -
105A ILE* 3.9 26.7 - - + -
107A ILE* 3.7 5.8 - - + +
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Residues in contact with ILE 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 TRP* 2.9 54.6 + - + +
59A ASP* 3.3 17.0 - - - +
61A ALA* 1.3 76.1 - - - +
63A GLN* 1.3 62.0 + - + +
65A GLY 3.9 0.2 - - - -
66A PHE* 3.0 27.9 + - + +
89A VAL* 4.1 25.6 - - + +
90A THR 5.7 0.4 - - - -
91A SER* 4.7 5.6 - - - -
105A ILE* 5.5 0.6 - - - +
107A ILE* 4.0 18.6 - - + +
176A THR* 5.4 0.2 - - - +
182A PRO* 3.8 37.7 - - + -
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP 3.8 8.1 - - - +
60A SER* 3.0 31.6 + - - +
62A ILE* 1.3 82.1 - - + +
64A THR* 1.3 69.6 + - - +
66A PHE* 3.4 4.8 + - - +
67A THR* 3.0 30.9 + - - +
182A PRO* 5.3 6.5 - - + -
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Residues in contact with THR 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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53A VAL* 4.5 14.6 - - + -
60A SER* 2.8 28.3 + - - -
61A ALA* 3.5 10.4 - - - -
63A GLN* 1.3 80.5 + - - +
65A GLY* 1.3 63.7 + - - +
66A PHE 3.5 0.2 + - - -
67A THR* 3.6 11.1 + - - -
68A LYS* 3.7 33.0 + - - +
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Residues in contact with GLY 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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51A THR* 3.7 21.3 - - - +
53A VAL* 5.3 3.6 - - - +
61A ALA 2.6 20.7 + - - -
62A ILE 4.0 0.7 - - - -
64A THR* 1.3 74.4 - - - +
66A PHE* 1.3 63.4 + - - +
68A LYS* 3.4 2.6 + - - -
69A LEU* 3.2 25.8 + - - +
107A ILE* 4.1 17.0 - - - -
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Residues in contact with PHE 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 ILE* 3.0 23.7 + - + +
63A GLN* 4.0 4.7 - - - +
64A THR 3.3 0.2 - - - -
65A GLY* 1.3 76.5 - - - +
67A THR* 1.3 56.5 + - - +
69A LEU* 3.2 3.8 + - - +
70A ASN* 2.6 53.3 + - + +
85A MET* 3.6 24.7 - - + -
89A VAL* 3.6 28.9 - - + -
107A ILE* 4.2 3.9 - - - +
109A LEU* 3.9 19.5 - - + -
182A PRO* 5.3 1.6 - - + -
183A VAL* 3.4 51.4 - - + -
185A LEU* 4.9 0.2 - - + -
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Residues in contact with THR 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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63A GLN* 3.0 17.7 + - - +
64A THR* 3.7 11.6 - - - -
66A PHE* 1.3 81.8 - - - +
68A LYS* 1.3 60.8 + - + +
70A ASN* 3.3 6.1 + - - +
71A SER* 3.0 32.5 + - - +
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Residues in contact with LYS 68 (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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51A THR* 4.0 19.4 + - + +
52A SER 5.2 1.8 + - - -
53A VAL* 4.8 11.3 - - + +
64A THR* 3.7 30.9 + - - +
65A GLY* 3.4 4.9 + - - +
66A PHE 3.3 0.2 - - - -
67A THR* 1.3 76.1 - - + +
69A LEU* 1.3 67.1 + - - +
71A SER* 3.2 6.6 + - - -
72A TYR* 3.2 19.2 + - - +
124A GLU* 4.2 24.6 - - - +
126A ASP* 2.7 31.9 + - - +
127A VAL* 4.1 17.8 - - + +
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Residues in contact with LEU 69 (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 VAL* 3.5 29.4 - - + +
50A SER 3.8 20.9 - - - +
51A THR* 4.0 7.4 - - + +
65A GLY 3.2 11.7 + - - +
66A PHE* 3.6 7.6 - - - +
68A LYS* 1.3 75.7 - - - +
70A ASN* 1.3 64.5 + - - +
72A TYR* 3.1 16.3 + - - +
73A ILE* 3.2 16.3 + - - +
89A VAL* 5.3 0.2 - - + -
107A ILE* 3.3 44.6 - - + +
108A SER* 3.6 16.4 - - - +
109A LEU* 3.8 20.4 - - + +
127A VAL* 4.4 4.0 - - + -
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Residues in contact with ASN 70 (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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66A PHE* 2.6 38.7 + - + +
67A THR* 3.7 6.3 + - - +
69A LEU* 1.3 73.5 - - - +
71A SER* 1.3 61.3 + - - +
73A ILE* 3.3 7.3 + - - +
74A GLN* 3.0 61.6 + - - +
85A MET* 3.2 21.1 - - - +
109A LEU* 4.5 3.5 - - - +
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Residues in contact with SER 71 (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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67A THR* 3.0 20.7 + - - +
68A LYS* 3.4 11.7 - - - -
69A LEU 3.1 0.2 - - - -
70A ASN* 1.3 77.9 - - - +
72A TYR* 1.3 60.7 + - - +
74A GLN* 3.4 7.1 + - - +
75A GLY 3.4 6.8 + - - -
76A LYS* 3.0 36.3 + - - +
124A GLU* 4.2 13.8 + - - -
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Residues in contact with TYR 72 (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 VAL* 3.8 26.2 - - + -
68A LYS 3.2 7.6 + - - +
69A LEU* 3.1 11.3 + - - +
71A SER* 1.3 80.2 - - - +
73A ILE* 1.3 72.6 + - + +
75A GLY 3.4 3.3 + - - -
76A LYS 3.7 10.2 + - - +
77A ASN* 3.1 42.6 + - + -
83A ILE* 3.4 22.1 - - + +
111A ILE* 4.5 6.3 - - + +
119A PRO* 3.9 3.5 - - - +
120A PRO* 2.5 45.6 + - + +
122A PRO* 3.7 32.5 - - + -
127A VAL* 4.5 8.5 - - + -
129A ILE* 3.6 13.5 - - + +
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Residues in contact with ILE 73 (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 VAL* 4.7 4.7 - - + -
69A LEU 3.2 9.9 + - - +
70A ASN* 3.5 11.9 - - - +
72A TYR* 1.3 93.3 - - + +
74A GLN* 1.3 72.6 + - - +
75A GLY 3.2 0.4 - - - -
81A MET 4.5 0.4 - - - -
82A LYS* 3.6 1.9 - - - +
83A ILE* 2.7 59.8 + - + +
84A LYS 4.5 1.1 - - - +
85A MET* 3.5 55.4 - - + -
109A LEU* 4.2 15.7 - - + -
111A ILE* 6.4 0.9 - - + -
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Residues in contact with GLN 74 (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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70A ASN* 3.0 55.4 + - - +
71A SER* 3.4 7.8 + - - +
72A TYR 3.3 0.2 - - - -
73A ILE* 1.3 91.9 - - - +
75A GLY* 1.3 56.0 + - - +
76A LYS 4.0 0.2 - - - -
82A LYS* 2.9 51.2 + - - +
83A ILE 5.6 0.6 + - - -
85A MET* 4.7 3.2 - - - +
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Residues in contact with GLY 75 (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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71A SER 3.4 0.6 + - - -
72A TYR 3.4 1.0 + - - -
73A ILE 3.2 4.0 - - - -
74A GLN* 1.3 82.4 - - - +
76A LYS* 1.3 58.6 + - - +
77A ASN* 2.8 16.4 + - - +
80A GLU* 3.2 28.2 - - - +
81A MET 3.6 20.4 - - - -
82A LYS* 4.6 0.4 - - - -
123A LEU* 5.3 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