Contacts of the strand formed by residues 115 - 124 (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 SER 115 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D TYR* 5.7 0.5 - - - +
60D GLY 2.9 16.3 - - - +
62D ALA* 2.9 19.4 + - - +
63D GLU 3.0 22.2 + - - -
64D VAL* 3.5 14.8 - - - +
75D THR* 3.4 18.4 - - - -
77D GLU* 6.1 4.3 - - - -
114D THR* 1.3 72.9 + - - +
116D ILE* 1.3 64.3 + - - +
117D THR* 4.2 7.2 + - - -
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Residues in contact with ILE 116 (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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58D VAL* 4.1 14.1 - - + -
59D TYR 3.4 15.0 - - - +
60D GLY 3.7 16.2 - - - +
61D PRO* 4.4 8.7 - - + -
74D ALA* 4.9 14.4 - - + -
75D THR 3.0 7.9 + - - +
76D LEU* 3.4 26.3 - - + +
77D GLU* 2.9 25.5 + - - +
106D VAL* 4.7 9.9 - - + -
108D GLY* 6.4 0.2 - - - -
111D HIS* 5.9 4.5 - - + -
114D THR* 5.0 5.2 - - + -
115D SER* 1.3 77.2 - - - +
117D THR* 1.3 61.8 + - - +
118D VAL* 4.4 2.9 - - + -
141D LEU* 4.7 3.6 - - + -
146D VAL* 3.7 34.8 - - + -
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Residues in contact with THR 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 4.0 19.1 + - + +
57D GLY 4.1 0.5 - - - +
58D VAL* 3.4 5.9 - - - +
59D TYR* 3.0 48.6 + - + +
77D GLU* 3.6 18.6 - - + +
79D ILE* 4.8 6.7 - - + -
115D SER* 4.1 8.7 + - - -
116D ILE* 1.3 75.4 + - - +
118D VAL* 1.3 64.1 + - - +
119D VAL* 3.7 22.7 - - + +
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D ALA* 5.6 0.2 - - + -
58D VAL* 3.8 29.4 - - + -
76D LEU* 4.1 19.3 - - + -
77D GLU 2.9 16.9 + - - +
78D VAL* 3.3 15.4 - - + +
79D ILE 2.9 27.0 + - - +
98D ILE* 5.3 2.2 - - + -
102D CYS* 5.5 4.5 - - - -
116D ILE* 4.4 0.9 - - + -
117D THR* 1.3 75.8 - - - +
119D VAL* 1.3 62.7 + - - +
120D LEU* 3.7 21.0 - - + +
137D ALA* 4.5 11.0 - - + -
141D LEU* 3.8 19.3 - - + -
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Residues in contact with VAL 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 3.8 14.4 - - - +
84A GLN* 3.7 33.2 - - + -
85A MET* 3.7 36.6 - - + +
55D LEU 4.0 0.7 - - - +
56D ALA* 3.3 5.0 - - - +
57D GLY 2.9 41.8 + - - +
59D TYR* 5.7 3.1 - - + +
79D ILE* 3.6 13.2 - - + +
81D ARG* 6.1 1.8 - - - -
117D THR* 3.7 13.0 - - + +
118D VAL* 1.3 76.9 - - - +
120D LEU* 1.3 68.9 + - - +
121D GLN* 5.9 0.2 - - + -
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Residues in contact with LEU 120 (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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54D VAL* 4.5 7.0 - - + -
55D LEU 3.7 2.9 - - - +
56D ALA* 4.3 15.7 - - + -
78D VAL* 4.9 6.1 - - + -
79D ILE 2.9 13.1 + - - +
80D LEU* 3.6 20.1 - - + -
81D ARG* 3.0 29.1 + - - +
98D ILE* 5.1 13.5 - - + -
118D VAL* 3.7 27.1 - - + +
119D VAL* 1.3 86.9 - - - +
121D GLN* 1.3 61.1 + - - +
122D VAL 4.2 0.2 - - - -
133D CYS* 3.6 45.1 - - + +
137D ALA* 4.6 6.7 - - + -
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Residues in contact with GLN 121 (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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56A LEU* 4.2 18.1 - - + +
83A SER* 4.3 10.3 + - - +
85A MET* 4.0 20.6 - - + +
137A HIS* 3.3 46.1 + - - -
139A LEU* 4.6 13.7 - - + -
54D VAL* 4.2 1.9 - - - -
55D LEU* 3.2 31.1 + - + +
81D ARG* 3.6 32.8 + - - +
82D PRO 3.9 5.1 + - - -
83D LYS* 4.1 5.5 - - - +
120D LEU* 1.3 75.2 - - - +
122D VAL* 1.3 66.1 + - - +
123D VAL* 3.2 7.0 + - + +
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Residues in contact with VAL 122 (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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56A LEU* 4.3 2.4 - - - +
53D SER 4.4 4.0 - - - +
54D VAL* 5.0 4.5 - - + -
80D LEU* 4.2 20.4 - - + -
81D ARG 3.0 18.1 + - - +
82D PRO* 3.9 17.9 - - + -
83D LYS* 3.6 26.5 + - + +
91D GLU* 6.0 1.3 - - - +
121D GLN* 1.3 73.4 + - - +
123D VAL* 1.3 63.1 + - - +
124D SER 4.2 15.0 - - - +
125D ASP* 4.4 8.1 - - + +
129D LEU* 4.1 34.8 - - + -
133D CYS* 5.0 8.1 - - - -
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Residues in contact with VAL 123 (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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45A CYS* 4.1 16.1 - - - -
47A ILE* 4.9 10.3 - - + -
56A LEU* 4.5 22.8 - - + +
139A LEU* 5.7 2.7 - - + -
53D SER* 3.0 33.2 + - - +
55D LEU* 4.2 22.2 - - + +
83D LYS* 3.0 28.3 + - - +
121D GLN* 3.2 12.7 + - + +
122D VAL* 1.3 73.3 - - - +
124D SER* 1.3 63.0 + - - +
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Residues in contact with SER 124 (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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41A THR* 3.5 22.1 + - - -
42A ASP* 5.1 3.5 + - - -
45A CYS* 6.0 1.3 - - - -
51D ASP* 3.0 25.5 + - - +
52D THR* 2.4 28.2 + - - -
53D SER* 2.9 27.3 + - - +
83D LYS* 4.4 5.6 - - - +
122D VAL* 4.3 5.4 - - - +
123D VAL* 1.3 82.8 - - - +
125D ASP* 1.3 56.1 + - - +
126D ALA* 4.8 1.2 - - - +
129D LEU* 4.6 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