Contacts of the strand formed by residues 111 - 119 (chain A) in PDB entry 4MXV
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 HIS 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLN* 3.3 45.3 + - + +
103A LEU 3.5 2.5 - - - -
104A PHE* 4.1 24.0 - + + +
105A SER* 4.9 1.3 - - - -
109A PRO* 2.7 37.3 + - - +
110A PHE* 1.3 88.3 - - + +
112A VAL* 1.3 60.6 + - - +
113A PRO* 3.8 6.3 - - - +
148A SER* 4.3 10.2 + - - -
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Residues in contact with VAL 112 (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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102A GLN* 3.6 2.3 - - - -
103A LEU* 2.9 60.9 + - + +
105A SER* 4.8 11.3 - - - -
111A HIS* 1.3 73.4 - - - +
113A PRO* 1.3 79.7 - - + +
114A LEU* 4.1 1.5 - - + +
51D ARG* 4.4 24.0 - - + +
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Residues in contact with PRO 113 (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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100A GLU* 3.5 26.0 - - + +
101A VAL 4.1 2.9 - - - +
102A GLN* 4.7 0.7 - - - -
111A HIS 3.8 7.0 - - - +
112A VAL* 1.3 98.7 - - + +
114A LEU* 1.3 67.0 + - - +
116A SER* 4.1 6.3 - - - +
51D ARG* 4.8 5.2 - - - +
161D PRO* 5.0 5.4 - - - +
162D SER* 3.8 25.9 + - - +
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Residues in contact with LEU 114 (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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75A VAL* 5.3 1.1 - - + -
101A VAL* 2.8 24.5 + - + +
102A GLN 4.4 0.7 - - - -
103A LEU* 3.9 24.2 - - + +
112A VAL* 4.1 7.0 - - + +
113A PRO* 1.3 79.9 - - - +
115A LEU* 1.3 73.5 + - + +
139A PHE* 3.6 44.9 - - + -
141A LEU* 4.9 3.1 - - + -
147A LEU* 3.8 28.9 - - + -
32D HIS* 5.3 0.7 + - - -
51D ARG* 3.6 31.9 - - - +
161D PRO 4.2 4.3 - - - +
162D SER* 3.6 14.6 - - - -
165D PHE* 4.8 0.5 - - - -
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Residues in contact with LEU 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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75A VAL* 3.3 27.1 - - + +
100A GLU* 3.1 6.2 - - - +
101A VAL* 2.8 45.8 + - + -
113A PRO 3.8 0.4 - - - -
114A LEU* 1.3 95.0 - - + +
116A SER* 1.3 62.2 + - - +
135A HIS* 3.3 39.6 + - + +
136A GLY* 3.8 2.5 - - - -
137A ALA* 3.8 9.4 - - + +
139A PHE* 3.7 20.4 - - + -
162D SER* 3.7 4.9 - - - -
165D PHE* 3.7 28.9 - - + -
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Residues in contact with SER 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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99A HIS 3.7 5.6 - - - -
100A GLU* 3.9 17.4 - - - +
113A PRO* 4.1 4.2 - - - +
115A LEU* 1.3 74.9 + - - +
117A SER* 1.3 68.2 + - - +
118A GLN* 6.3 1.3 - - - -
135A HIS* 3.9 3.5 + - - -
78D GLN* 3.6 10.4 + - - +
80D VAL* 5.1 1.9 - - - +
162D SER* 2.9 41.5 + - - +
163D THR* 3.9 16.4 - - - +
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Residues in contact with SER 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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98A ALA* 3.3 3.8 - - - +
99A HIS 3.1 18.3 + - - +
116A SER* 1.3 78.4 + - - +
118A GLN* 1.3 66.1 + - - +
133A MET* 3.2 43.3 - - - +
134A TYR 4.7 1.7 + - - -
135A HIS* 3.0 21.9 + - - -
78D GLN* 4.3 3.6 + - - -
132D SER* 4.3 18.4 + - - -
163D THR* 5.8 0.7 - - - -
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Residues in contact with GLN 118 (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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96A TYR* 3.0 38.2 + - + +
97A LEU 3.4 9.6 - - - +
98A ALA* 4.4 1.1 - - + +
116A SER* 6.3 1.3 - - - -
117A SER* 1.3 81.1 - - - +
119A LYS* 1.3 67.4 + - - +
120A MET* 5.0 6.2 - - + +
133A MET* 4.5 7.4 - - - +
130D LEU* 3.4 33.8 - - + +
132D SER* 5.4 7.1 - - - -
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Residues in contact with LYS 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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96A TYR* 4.0 4.7 - - - -
97A LEU* 3.0 41.3 + - + +
118A GLN* 1.3 78.5 - - - +
120A MET* 1.3 70.5 + - - +
121A VAL 3.9 1.8 - - - +
131A HIS* 3.6 48.8 + - + +
133A MET* 4.7 6.3 - - + -
130D LEU* 3.3 34.7 + - + +
131D HIS* 4.4 13.8 + - - +
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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