Contacts of the strand formed by residues 97 - 103 (chain D) 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 LEU 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D PHE* 3.5 43.3 - - + -
95D LEU* 3.8 21.1 - - + -
96D TYR* 1.3 85.4 - - - +
98D ALA* 1.3 64.5 + - - +
118D GLN* 3.4 3.8 - - - +
119D LYS* 3.1 41.3 + - + +
121D VAL* 4.1 15.0 - - + -
129D TRP* 3.6 21.1 - - + -
131D HIS* 4.5 13.7 - - + -
133D MET* 5.1 1.8 - - - -
152D ASP* 3.4 10.1 - - - +
153D GLY* 4.0 11.9 - - - +
156D HIS* 4.9 1.3 - - + -
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Residues in contact with ALA 98 (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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81D PHE* 3.5 3.8 - - - -
96D TYR* 3.7 19.3 - - + +
97D LEU* 1.3 76.9 - - - +
99D HIS* 1.3 64.7 + - - +
100D GLU* 6.0 2.2 - - + +
117D SER 3.4 14.1 - - - +
118D GLN* 4.6 1.1 - - + -
133D MET* 4.1 4.3 - - - -
150D HIS 4.7 0.2 - - - -
151D THR* 3.4 7.4 - - - +
152D ASP* 2.9 48.2 + - - +
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Residues in contact with HIS 99 (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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43D LEU* 4.6 0.7 - - + -
45D TRP* 4.4 7.0 - + - -
77D SER* 2.9 34.2 + - - -
78D GLN* 4.6 0.4 - - - -
79D VAL* 3.4 40.7 - - + +
81D PHE* 4.6 0.2 - - + -
98D ALA* 1.3 77.8 - - - +
100D GLU* 1.3 63.7 + - - +
117D SER 3.3 27.4 + - - +
133D MET* 3.5 18.9 - - + +
135D HIS* 3.9 15.5 + + - -
149D THR* 3.6 29.6 - - + +
150D HIS 3.4 6.5 + - - -
151D THR* 2.6 26.9 + - - +
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Residues in contact with GLU 100 (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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98D ALA* 6.0 2.3 - - + +
99D HIS* 1.3 80.0 - - - +
101D VAL* 1.3 67.4 + - - +
102D GLN* 3.3 37.2 + - + +
111D HIS* 5.8 0.3 - - - +
112D VAL 5.1 0.2 - - - -
113D PRO* 3.7 26.2 - - + +
115D LEU 3.3 11.9 - - - +
116D SER* 4.3 7.3 + - - +
135D HIS* 5.1 0.2 - - - -
149D THR* 3.1 29.3 - - - -
150D HIS* 2.9 23.4 + - + +
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Residues in contact with VAL 101 (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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75D VAL* 4.0 15.9 - - + -
76D TYR 5.0 0.7 - - - -
77D SER* 3.6 31.4 - - - +
99D HIS* 5.0 0.2 - - - +
100D GLU* 1.3 75.9 - - - +
102D GLN* 1.3 61.1 - - - +
113D PRO* 3.8 0.5 - - - +
114D LEU* 2.8 43.9 + - + +
115D LEU* 2.9 33.8 + - + +
135D HIS* 4.8 2.2 - - + -
147D LEU* 5.0 2.0 - - + -
148D SER 3.5 9.9 - - - +
149D THR* 4.1 7.4 - - + -
166D PHE* 3.8 20.9 - - + -
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Residues in contact with GLN 102 (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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100D GLU* 3.3 33.6 + - + +
101D VAL* 1.3 79.3 - - - +
103D LEU* 1.3 64.1 + - - +
104D PHE 3.9 0.4 - - - -
111D HIS* 2.9 41.0 + - + +
112D VAL 3.4 13.9 - - - +
113D PRO* 4.4 0.2 - - - -
114D LEU* 4.1 4.6 - - - +
147D LEU* 3.8 6.1 - - - -
148D SER* 2.9 42.2 + - - +
149D THR 5.3 0.7 - - - -
150D HIS* 3.7 32.8 + - - +
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Residues in contact with LEU 103 (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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51B ARG* 3.8 26.0 - - - +
102D GLN* 1.3 75.4 - - - +
104D PHE* 1.3 70.7 + - - +
111D HIS* 4.1 1.9 - - - -
112D VAL* 2.9 35.4 + - + +
114D LEU* 4.1 16.6 - - + -
141D LEU* 4.0 19.5 - - + -
145D ASP* 4.0 30.5 - - + +
146D GLN 3.7 13.7 - - - +
147D LEU* 3.8 18.4 - - + -
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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