Contacts of the strand formed by residues 114 - 123 (chain A) in PDB entry 6ARQ
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A LYS* 4.0 10.8 - - - -
62A THR* 5.6 3.6 - - - -
112A VAL 3.5 2.2 + - - -
113A SER* 1.3 74.4 + - - +
115A ARG* 1.3 59.6 + - - -
116A TYR* 3.5 13.9 - - - -
133A ASN* 3.9 9.2 - - - -
134A LEU* 2.9 31.6 + - - +
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Residues in contact with ARG 115 (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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30A GLU* 2.8 30.6 + - - -
60A LYS* 3.4 8.4 - - - +
61A VAL* 2.9 64.0 + - + +
62A THR* 5.5 0.4 - - - +
114A GLY* 1.3 69.9 - - - -
116A TYR* 1.3 56.3 + - - +
131A ILE* 3.8 24.2 - - + +
132A TYR 3.4 3.1 - - - -
133A ASN* 3.5 28.2 + - + +
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Residues in contact with TYR 116 (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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43A LEU* 3.9 23.1 - - + -
58A TRP* 4.0 9.0 - - + -
59A SER 3.4 2.7 - - - +
60A LYS* 3.7 30.7 + - + +
68A ILE* 3.7 30.5 - - + -
103A LEU* 3.9 11.9 - - + -
105A LEU* 4.5 8.9 - - + +
112A VAL* 2.7 44.7 + - + +
114A GLY 3.5 19.3 - - - -
115A ARG* 1.3 71.0 - - - +
117A GLU* 1.3 60.2 + - - +
130A LYS 3.9 1.2 - - - +
131A ILE* 3.6 1.5 - - - -
132A TYR* 2.8 43.0 + - - +
134A LEU* 4.0 19.5 - - + -
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Residues in contact with GLU 117 (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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57A GLN* 4.0 0.7 - - - +
58A TRP* 3.4 5.6 - - - -
59A SER* 2.8 48.8 + - - +
61A VAL* 4.5 23.3 - - + +
65A ILE* 6.0 1.2 - - - +
115A ARG 4.2 0.4 - - - -
116A TYR* 1.3 72.8 - - - +
118A CYS* 1.3 64.9 + - - +
119A MET* 3.5 30.1 + - - +
129A THR* 3.6 23.6 - - + +
130A LYS 3.5 3.4 - - - +
131A ILE* 3.7 25.8 - - + +
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Residues in contact with CYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A CYS* 2.0 51.4 - - - -
57A GLN 3.3 10.1 - - - +
58A TRP* 3.6 19.9 - - + -
101A TRP* 4.0 5.2 - - + -
117A GLU* 1.3 77.3 - - - +
119A MET* 1.3 58.1 + - - +
120A LEU* 4.2 11.0 - - - -
129A THR* 3.5 6.5 - - - +
130A LYS* 3.0 35.7 + - - -
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Residues in contact with MET 119 (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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55A GLN 4.0 0.3 - - - +
56A MET* 3.2 6.9 - - - +
57A GLN* 3.0 49.4 + - + +
117A GLU* 3.5 19.3 - - - +
118A CYS* 1.3 73.1 - - - +
120A LEU* 1.3 61.9 + - - +
121A VAL* 4.1 7.5 + - + +
127A ILE* 3.8 26.7 - - + -
128A GLN 3.5 3.1 - - - +
129A THR* 4.2 7.4 - - + +
124D LEU* 4.7 12.8 - - + -
132D SER* 3.3 37.0 - - - -
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A CYS* 3.7 27.4 - - + +
46A GLN 5.4 0.4 - - - +
47A THR* 3.8 32.1 - - + -
55A GLN 3.9 2.0 - - - -
56A MET* 3.8 38.1 - - + -
99A SER* 4.9 0.4 - - - +
101A TRP* 4.0 13.7 - - + -
118A CYS* 4.2 8.3 - - - -
119A MET* 1.3 73.6 - - - +
121A VAL* 1.3 61.9 + - - +
122A LEU* 3.7 13.8 + - + +
126A GLY 3.4 2.9 - - - +
127A ILE* 3.4 2.8 - - - -
128A GLN* 2.8 51.5 + - + +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.8 2.4 - - - +
54A VAL* 2.8 38.1 + - + -
55A GLN* 2.8 28.5 + - + +
56A MET* 5.4 0.3 - - - +
119A MET* 4.9 8.3 - - + +
120A LEU* 1.3 72.6 - - - +
122A LEU* 1.3 62.0 + - - +
126A GLY 3.7 2.9 - - - +
127A ILE* 3.9 21.3 - - + -
63D GLN* 3.7 36.3 - - - +
126D VAL* 4.0 26.5 - - + -
132D SER* 4.7 7.9 - - - +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A THR* 3.5 16.2 - - + +
48A GLN 3.6 19.3 - - - +
49A THR* 3.7 14.6 - - - -
52A PHE 3.8 3.4 - - - -
53A PHE* 3.7 24.9 - - + -
54A VAL* 4.1 4.8 - - - +
56A MET* 5.8 0.2 - - + -
120A LEU* 3.7 25.1 - - + +
121A VAL* 1.3 80.9 - - - +
123A TYR* 1.3 62.6 + - - +
124A PRO* 4.1 0.5 - - - +
125A GLU* 3.8 20.0 - - + +
126A GLY* 2.8 34.5 + - - +
128A GLN* 3.4 25.1 - - - +
63D GLN* 4.8 1.7 + - - +
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Residues in contact with TYR 123 (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 THR* 3.3 4.5 + - - -
51A GLY* 3.4 3.3 - - - -
52A PHE* 2.9 60.3 + + + +
54A VAL* 3.8 6.3 - - + +
122A LEU* 1.3 73.0 - - - +
124A PRO* 1.4 78.6 - - + +
125A GLU* 3.5 3.1 - - - -
63D GLN* 3.8 16.8 - - - -
77D VAL* 4.2 17.6 - - + +
79D HIS* 3.7 24.5 - + + -
82D GLN* 3.5 36.4 - - + +
83D GLY 4.4 8.5 + - - -
84D PRO 5.5 0.5 + - - -
85D SER* 4.4 14.6 - - - -
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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