Contacts of the strand formed by residues 52 - 62 (chain D) in PDB entry 6H25
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 THR 52 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D ARG* 4.6 2.0 - - - +
48D LEU* 3.5 4.3 - - - +
49D GLN* 2.9 54.0 + - + +
51D ASP* 1.3 80.7 - - - +
53D SER* 1.3 63.2 + - - +
54D VAL* 5.1 0.9 - - - +
124D SER 2.4 27.3 + - - -
125D ASP* 3.7 1.7 - - - -
126D ALA* 3.3 25.5 + - - +
127D GLY 4.1 14.9 + - - +
128D SER 4.8 0.9 - - - +
129D LEU* 4.1 10.9 - - - +
132D CYS* 4.0 17.0 - - + -
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Residues in contact with SER 53 (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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46D SER* 4.6 3.5 + - - -
47D PHE 3.5 6.3 - - - -
48D LEU* 3.9 26.0 - - - +
51D ASP 4.5 1.3 - - - -
52D THR* 1.3 79.5 + - - +
54D VAL* 1.3 65.3 + - - +
122D VAL* 4.4 0.2 - - - -
123D VAL* 3.0 29.1 + - - +
124D SER* 2.9 45.9 + - - +
132D CYS* 4.5 0.2 - - - -
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Residues in contact with VAL 54 (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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45D ALA 3.8 1.6 - - - +
46D SER* 3.7 1.5 - - - -
47D PHE* 3.0 31.4 + - - -
52D THR* 5.1 0.4 - - - +
53D SER* 1.3 82.1 + - - +
55D LEU* 1.3 67.8 + - - +
120D LEU* 4.5 10.5 - - + -
121D GLN 4.2 7.0 - - - +
122D VAL* 5.0 6.5 - - + -
129D LEU* 4.6 12.3 - - + +
132D CYS* 3.7 27.3 - - + +
133D CYS* 3.7 37.0 - - - -
136D ALA* 3.8 19.0 - - + +
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Residues in contact with LEU 55 (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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54A ARG* 4.7 6.1 - - - +
85A MET* 4.2 10.2 - - + +
139A LEU* 3.6 31.4 - - + -
37D LEU* 5.0 5.6 - - + -
38D LEU* 3.8 28.9 - - + -
44D SER 5.2 0.4 - - - -
45D ALA 3.3 26.0 - - - +
46D SER* 3.7 16.4 - - - +
54D VAL* 1.3 76.5 - - - +
56D ALA* 1.3 66.8 + - - +
119D VAL 4.0 0.2 - - - +
120D LEU* 3.7 2.6 - - - -
121D GLN* 3.2 34.2 + - + +
123D VAL* 4.2 17.8 - - + +
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Residues in contact with ALA 56 (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 LEU* 5.8 0.4 - - - +
44D SER* 3.4 3.6 - - - -
45D ALA 2.9 33.0 + - - +
55D LEU* 1.3 79.8 - - - +
57D GLY* 1.3 58.3 + - - +
58D VAL* 5.4 1.8 - - + -
119D VAL 3.3 9.4 - - - +
120D LEU* 4.3 12.8 - - + -
136D ALA* 3.7 37.0 - - + +
137D ALA* 4.3 2.9 - - - +
140D ALA* 3.9 9.2 - - + +
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Residues in contact with GLY 57 (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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85A MET* 4.3 22.4 - - - +
38D LEU* 5.7 1.1 - - - -
41D PRO* 4.7 7.6 - - - -
43D GLY 3.4 9.0 - - - -
44D SER* 4.7 1.8 - - - -
56D ALA* 1.3 72.7 - - - +
58D VAL* 1.3 62.0 + - - -
59D TYR* 4.3 1.3 - - - -
119D VAL* 2.9 41.1 + - - +
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Residues in contact with VAL 58 (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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41D PRO* 4.5 0.6 - - - +
42D ASP* 3.3 8.3 + - - +
43D GLY 3.1 28.5 + - - +
56D ALA 4.4 0.4 + - - -
57D GLY* 1.3 79.1 - - - +
59D TYR* 1.3 78.0 + - - +
116D ILE* 4.1 13.0 - - + -
117D THR 3.4 7.0 - - - +
118D VAL* 3.8 20.6 - - + -
140D ALA* 3.7 30.7 - - + +
141D LEU* 3.8 24.5 - - + -
144D ALA* 4.3 12.8 - - + +
146D VAL* 5.1 1.6 - - + -
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Residues in contact with TYR 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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84A GLN* 3.3 21.9 + - + -
85A MET* 2.8 27.8 + - - -
86A ALA 3.8 0.2 - - - -
87A ALA* 3.1 21.5 + - - -
88A PRO* 3.3 32.4 - - + +
40D ARG* 4.5 3.9 - - - +
41D PRO* 3.6 33.4 - - + -
42D ASP* 3.4 8.7 - - - +
57D GLY 4.3 1.3 - - - -
58D VAL* 1.3 87.3 - - - +
60D GLY* 1.3 69.3 + - - +
62D ALA* 5.4 7.4 - - + -
115D SER 5.7 0.2 - - - +
116D ILE* 3.4 11.4 - - - +
117D THR* 3.0 31.3 + - + +
119D VAL* 5.7 1.8 - - + +
108G ARG* 5.8 2.7 - - - +
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Residues in contact with GLY 60 (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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42D ASP* 2.5 27.0 + - - +
58D VAL* 5.1 0.7 - - - -
59D TYR* 1.3 78.5 - - - +
61D PRO* 1.3 76.9 - - - +
62D ALA* 3.3 3.8 + - - +
115D SER 2.9 18.0 - - - +
116D ILE* 3.7 6.4 - - - -
144D ALA* 5.4 3.4 - - - -
146D VAL* 4.6 9.6 - - - -
108G ARG* 4.6 2.7 - - - +
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Residues in contact with PRO 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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60D GLY* 1.3 82.2 - - - +
62D ALA* 1.3 59.7 + - - +
111D HIS* 4.5 20.6 - - + +
114D THR* 3.2 24.9 - - + +
115D SER 4.0 2.0 - - - +
116D ILE* 4.4 6.7 - - + -
144D ALA 6.1 0.9 - - - +
145D GLY 6.4 0.2 - - - -
146D VAL* 4.6 13.9 - - + -
108G ARG* 3.5 37.1 + - + -
109G TYR 5.5 0.6 - - - +
110G VAL* 4.5 20.4 - - + -
135G GLY 4.4 5.0 - - - +
136G SER* 4.5 9.4 - - - +
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Residues in contact with ALA 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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59D TYR* 5.4 8.1 - - + -
60D GLY 4.0 5.2 - - - +
61D PRO* 1.3 75.3 - - - +
63D GLU* 1.3 62.8 + - - +
113D ARG 4.6 0.3 - - - +
114D THR* 2.7 20.1 + - - -
115D SER* 2.9 29.8 + - - +
108G ARG* 4.9 13.5 - - - +
135G GLY 4.7 3.1 - - - +
136G SER* 4.2 11.1 - - - +
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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