Contacts of the helix formed by residues 49 - 64 (chain A) in PDB entry 2GC5
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 GLY 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASN* 1.3 73.0 - - - +
50A LYS* 1.3 54.3 + - - +
52A SER* 3.6 0.9 - - - -
53A ALA* 2.8 37.2 + - - +
164A THR* 3.5 5.9 - - - +
260A TYR* 6.0 1.5 - - - -
263A ARG* 4.1 0.7 - - - -
264A ASN* 3.5 28.5 + - - -
900A SO4 2.8 25.3 + - - -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.6 30.8 - - + +
45A THR* 4.0 9.0 - - - -
46A GLY 3.7 25.3 + - - +
48A ASN* 3.3 3.8 + - - -
49A GLY* 1.3 76.6 - - - +
51A SER* 1.3 63.9 + - - +
54A ALA* 3.0 30.3 + - - +
73A SER* 4.7 9.1 + - - -
143A GLU* 3.8 21.3 - - + -
144A VAL* 2.8 30.3 + - + +
145A GLY 3.2 16.2 + - - -
164A THR* 3.5 11.0 + - - -
170A HIS* 5.2 3.2 - - - -
185A KCX 4.1 10.0 + - - +
900A SO4 5.6 0.4 - - - +
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS* 1.3 80.8 - - - +
52A SER* 1.3 60.6 + - - +
55A ASN* 3.0 31.8 + - - +
72A THR* 4.1 5.4 + - - -
73A SER* 4.2 16.9 - - - -
75A PHE* 5.1 2.9 - - - -
143A GLU* 2.7 33.5 + - - +
300A ARG* 4.2 6.7 - - - -
900A SO4 3.0 18.6 + - - -
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Residues in contact with SER 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.6 4.5 - - - -
51A SER* 1.3 72.7 - - - +
53A ALA* 1.3 62.3 + - - +
56A ALA* 3.1 20.8 + - - +
261A GLN* 2.8 40.4 + - - -
264A ASN* 3.7 6.3 - - - -
265A MET* 3.9 2.9 - - - +
297A TRP* 3.4 23.1 - - - -
300A ARG* 3.4 12.0 + - - +
900A SO4 2.8 26.7 + - - -
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.5 5.6 - - + -
49A GLY 2.8 21.8 + - - +
50A LYS 3.9 2.0 - - - +
52A SER* 1.3 70.0 - - - +
54A ALA* 1.3 68.0 + - - +
56A ALA* 3.3 3.5 + - - +
57A ILE* 2.9 32.9 + - + +
164A THR* 3.8 18.8 - - + -
264A ASN* 4.1 23.5 - - + +
267A ILE* 4.4 11.4 - - + -
268A ALA* 4.6 2.2 - - - +
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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
----------------------------------------------------------
44A VAL* 4.2 6.9 - - + +
50A LYS 3.0 18.3 + - - +
52A SER 3.4 0.2 - - - -
53A ALA* 1.3 75.9 - - - +
55A ASN* 1.3 62.7 + - - +
57A ILE* 3.3 7.5 + - - +
58A ALA* 3.0 24.8 + - - +
70A LEU* 4.0 4.9 - - + -
141A VAL* 3.8 24.2 - - + +
143A GLU* 3.4 32.3 - - + +
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Residues in contact with ASN 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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51A SER 3.0 18.4 + - - +
52A SER 3.7 4.0 - - - +
54A ALA* 1.3 77.1 - - - +
56A ALA* 1.3 58.1 + - - +
58A ALA* 3.4 4.3 + - - +
59A HIS* 2.9 58.5 + - - -
70A LEU* 3.6 15.5 - - + +
84A MET* 4.8 3.1 - - - +
87A HIS* 2.8 25.7 + - - -
143A GLU* 4.8 0.2 + - - -
296A HIS 3.4 18.4 + - - -
297A TRP* 3.6 18.7 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER 3.1 14.0 + - - +
55A ASN* 1.3 77.9 - - - +
57A ILE* 1.3 64.7 + - - +
59A HIS* 3.2 8.2 + - - +
60A VAL* 3.0 29.1 + - - +
265A MET* 3.7 24.7 - - + -
268A ALA* 3.4 24.0 - - + -
292A LEU* 4.6 7.9 - - + -
295A SER* 5.8 0.7 - - - -
297A TRP* 4.0 7.1 - - + -
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.8 29.4 - - + -
44A VAL* 4.3 17.0 - - + -
53A ALA* 2.9 33.4 + - + +
54A ALA* 3.6 9.0 - - - +
56A ALA* 1.3 73.4 - - - +
58A ALA* 1.3 64.3 + - - +
60A VAL* 3.4 3.4 + - - +
61A LEU* 3.0 32.2 + - + +
141A VAL* 4.1 8.7 - - + -
162A VAL* 4.3 4.0 - - + -
268A ALA* 3.5 30.5 - - - +
271A THR* 3.7 26.5 - - + +
272A ALA* 4.9 4.4 - - - +
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Residues in contact with ALA 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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54A ALA 3.0 13.2 + - - +
55A ASN 3.5 8.5 - - - +
57A ILE* 1.3 78.0 - - - +
59A HIS* 1.3 63.3 + - - +
61A LEU* 3.9 1.0 - - - +
62A GLU* 2.9 44.4 + - - +
68A VAL* 3.9 20.9 - - + -
70A LEU* 4.3 12.8 - - + -
87A HIS* 3.6 9.2 - - + -
141A VAL* 4.4 6.5 - - + +
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 2.9 53.3 + - - -
56A ALA* 3.2 8.9 + - - +
58A ALA* 1.3 73.1 - - - +
60A VAL* 1.3 56.6 + - + +
62A GLU* 3.5 9.1 + - - +
63A ALA* 3.0 28.8 + - - +
87A HIS* 3.2 33.7 + + + -
291A GLY* 3.4 21.9 + - - +
292A LEU* 5.4 0.7 - - + -
294A ALA* 4.2 8.5 + - - +
295A SER* 3.5 29.1 - - - -
296A HIS* 3.5 20.6 + + + +
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Residues in contact with VAL 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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56A ALA* 3.0 22.2 + - + +
57A ILE* 3.8 4.5 - - - +
59A HIS* 1.3 72.7 - - - +
61A LEU* 1.3 65.2 + - - +
63A ALA* 3.3 4.8 + - - +
64A SER* 3.2 19.9 + - - -
268A ALA* 5.5 1.1 - - + +
269A ILE* 5.2 8.7 - - + +
272A ALA* 3.6 28.0 - - + -
283A LEU* 3.9 9.7 - - + +
287A ASN 4.4 1.4 - - - +
288A ILE* 3.9 46.9 - - + +
291A GLY* 4.2 5.6 - - - -
292A LEU* 4.4 18.8 - - + +
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Residues in contact with LEU 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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42A ILE* 3.6 31.4 - - + -
57A ILE* 3.0 26.2 + - + +
60A VAL* 1.3 76.4 - - - +
62A GLU* 1.3 62.0 + - - +
64A SER* 2.8 24.5 + - - +
66A LEU* 3.3 24.0 + - + +
68A VAL* 3.9 16.2 - - + -
139A VAL* 4.3 11.0 - - + -
141A VAL* 5.2 2.5 - - + -
272A ALA* 4.0 27.4 - - + +
275A TYR* 4.0 25.6 - - + -
276A ALA* 5.2 3.4 - - + +
281A TRP* 5.3 0.7 - - + -
283A LEU* 4.6 7.6 - - + -
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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 ALA* 2.9 31.7 + - - +
59A HIS* 3.5 10.0 + - - +
61A LEU* 1.3 75.5 - - - +
63A ALA* 1.3 56.2 - - - +
65A GLY* 3.0 20.1 + - - -
66A LEU 3.5 10.3 - - - +
68A VAL* 3.7 14.7 - - + +
70A LEU* 5.6 0.7 - - - +
86A ASP* 3.4 46.1 + - + +
87A HIS* 2.9 36.2 + - - +
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Residues in contact with ALA 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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59A HIS 3.0 13.8 + - - +
60A VAL 3.6 5.6 - - - +
61A LEU 3.3 0.2 - - - -
62A GLU* 1.3 75.1 - - - +
64A SER* 1.3 60.1 + - - +
65A GLY* 3.2 2.5 + - - -
287A ASN* 3.3 38.5 + - - +
290A GLN* 4.3 13.7 + - + +
291A GLY* 3.7 12.6 - - - +
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Residues in contact with SER 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 VAL 3.2 5.9 + - - -
61A LEU* 2.8 20.5 + - - +
62A GLU 3.2 0.6 - - - -
63A ALA* 1.3 75.8 - - - +
65A GLY* 1.3 55.4 + - - +
66A LEU* 3.9 2.6 - - - +
281A TRP* 2.9 39.7 + - - -
282A PRO 4.1 3.6 - - - +
283A LEU* 3.5 29.7 - - - +
287A ASN* 3.6 18.2 - - - +
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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