Contacts of the strand formed by residues 58 - 72 (chain D) in PDB entry 2Q41
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 GLU 58 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A TRP* 3.4 9.6 - - - -
61A SER 3.2 11.4 - - - +
62A LEU* 3.9 10.1 - - + -
85A THR* 4.5 0.2 + - - -
86A TYR* 2.8 40.8 + - + -
101A ARG* 4.6 1.0 + - - -
268A PRO* 5.9 0.2 - - - +
50D GLU 4.5 0.3 - - - +
51D MSE 4.7 3.8 - - - +
52D SER 5.5 0.2 + - - -
55D TRP* 3.1 53.5 - - + +
56D PRO* 3.0 7.1 - - - +
57D GLY* 1.3 78.4 - - - +
59D ALA* 1.3 66.9 + - - +
60D HIS* 4.5 10.6 + - + +
240D LEU* 3.8 14.4 - - - +
271D PRO* 4.7 2.1 - - - +
272D SER* 4.1 18.4 + - - -
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Residues in contact with ALA 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TRP* 3.8 15.3 - - + -
61A SER* 2.7 43.9 + - - +
43D VAL* 5.1 4.3 - - + -
49D SER* 4.9 10.3 - - - -
50D GLU 3.6 17.9 - - - +
51D MSE 4.5 6.1 - - + -
55D TRP* 5.1 2.5 - - - -
58D GLU* 1.3 81.7 - - - +
60D HIS* 1.3 73.8 + - - +
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Residues in contact with HIS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA 3.5 3.8 - - - -
60A HIS* 3.2 38.9 + + + +
268A PRO 5.4 3.6 + - - -
48D PHE* 3.9 1.6 - - - +
49D SER* 3.6 0.2 - - - -
50D GLU* 3.0 42.2 + - + +
55D TRP* 5.7 0.2 - - - +
58D GLU* 4.5 10.2 + - + -
59D ALA* 1.3 83.1 - - - +
61D SER* 1.3 62.7 + - - +
62D LEU* 5.8 0.4 - - + -
96D ILE* 5.3 8.7 - - + +
268D PRO 4.2 8.0 + - - -
269D THR* 4.7 4.7 + - - +
270D TYR 3.6 10.6 + - - -
271D PRO* 3.5 34.4 - - + +
272D SER* 3.6 11.7 + - - -
273D GLY* 4.5 2.7 - - - -
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Residues in contact with SER 61 (chain D).
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* 3.1 6.9 - - - +
59A ALA 2.8 37.2 + - - -
61A SER* 4.2 10.4 + - - -
44D ILE* 4.4 10.4 - - - +
47D TRP* 3.7 20.0 - - - -
48D PHE* 3.1 13.0 - - - -
49D SER* 2.5 29.2 + - - -
59D ALA* 5.0 0.5 - - - +
60D HIS* 1.3 75.8 + - - +
62D LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY 3.1 12.6 - - - +
58A GLU* 3.8 9.4 - - + -
47D TRP* 3.6 5.8 - - - -
48D PHE* 3.1 29.3 + - + +
60D HIS* 5.8 0.4 - - + -
61D SER* 1.3 83.6 - - - +
63D LYS* 1.3 63.9 + - - +
64D VAL* 3.1 2.3 + - - +
81D PHE* 3.9 31.2 - - + -
83D SER* 4.9 3.8 - - - +
86D TYR* 3.7 41.7 - - + -
89D VAL* 4.6 3.8 - - + -
96D ILE* 4.1 24.5 - - + -
99D THR* 4.6 11.0 - - + -
269D THR* 4.8 3.4 - - + -
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Residues in contact with LYS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY* 2.8 24.3 + - - +
74C ASP* 3.9 27.3 + - - -
46D GLY 4.9 0.7 - - - +
47D TRP* 3.4 43.4 - - + +
62D LEU* 1.3 68.2 - - - +
64D VAL* 1.3 68.6 + - - +
65D GLU* 3.3 7.3 + - - +
81D PHE* 4.9 0.2 - - - -
83D SER* 4.0 3.8 + - - -
84D ALA* 3.3 36.7 + - + +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D CYS* 5.6 4.5 - - + -
46D GLY 3.4 20.3 + - - +
47D TRP 3.8 1.1 - - - -
48D PHE* 3.3 40.2 - - + +
62D LEU 3.1 1.1 + - - +
63D LYS* 1.3 75.9 - - - +
65D GLU* 1.3 64.3 + - - +
66D LYS* 3.9 11.2 - - - +
67D VAL* 3.9 26.5 - - + -
81D PHE* 4.1 21.1 - - + -
82D GLN 3.9 2.7 - - - -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D LYS* 3.3 7.0 + - - +
64D VAL* 1.3 75.2 - - - +
66D LYS* 1.3 65.2 + - + +
82D GLN* 2.7 38.3 + - + +
83D SER 4.1 7.4 - - - +
84D ALA* 4.1 22.4 - - - +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D VAL* 3.6 4.4 - - - -
65D GLU* 1.3 86.1 - - + +
67D VAL* 1.3 71.7 + - - +
68D LEU* 3.3 20.9 + - + +
82D GLN* 2.6 41.8 + - + +
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA* 5.3 17.7 - - - +
64D VAL* 3.9 19.3 - - + -
66D LYS* 1.3 79.2 - - - +
68D LEU* 1.3 63.3 + - - +
69D PHE 4.2 8.7 - - - +
70D GLN* 4.2 33.2 - - + +
79D ILE* 4.4 12.1 - - + -
81D PHE* 4.0 8.7 - - + +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D LYS* 3.7 40.8 - - + +
67D VAL* 1.3 73.6 - - - +
69D PHE* 1.3 56.8 + - - +
80D VAL* 2.9 35.7 + - + +
81D PHE 5.0 0.2 - - - -
82D GLN* 4.0 28.3 - - + +
88D LYS* 5.3 14.6 - - + -
163D PHE* 4.5 23.6 - - + +
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D VAL* 4.2 2.0 - - - +
68D LEU* 1.3 77.6 - - - +
70D GLN* 1.3 64.2 + - - +
71D GLY* 3.3 31.0 - - - -
78D VAL* 3.4 35.7 - - + -
79D ILE* 3.0 6.9 - - - +
80D VAL* 2.6 44.1 + - + -
155D MSE 4.1 19.5 - - + -
159D VAL* 3.7 11.4 - - + -
163D PHE* 3.3 38.8 - + + -
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Residues in contact with GLN 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ALA 4.8 17.7 + - - +
67D VAL* 4.2 19.2 - - + +
69D PHE* 1.3 78.9 - - - +
71D GLY* 1.3 58.9 + - - +
78D VAL 3.2 4.9 - - - -
79D ILE* 3.1 33.5 - - + +
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Residues in contact with GLY 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D PHE* 3.3 19.7 - - - -
70D GLN* 1.3 76.8 - - - +
72D LYS* 1.3 57.6 + - - +
77D ASP* 3.6 3.1 - - - +
78D VAL 2.7 38.5 + - - +
155D MSE 4.2 7.4 - - - -
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Residues in contact with LYS 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D GLY* 1.3 74.2 - - - +
73D SER* 1.3 70.7 + - - +
74D ASP 5.9 0.2 - - - -
75D TYR 4.8 1.8 + - - -
76D GLN* 3.6 24.0 - - - +
77D ASP* 3.0 29.5 + - + +
93D ASP* 5.4 0.2 + - - -
155D MSE 3.5 14.9 - - - +
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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