Contacts of the strand formed by residues 95 - 106 (chain H) in PDB entry 5M5X
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 TYR 95 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719A ILE* 3.2 25.2 - - + +
721A LYS* 3.2 24.8 - - - +
722A PRO* 4.1 10.3 - - + -
42H ILE* 3.6 18.2 - - + -
43H ASN* 2.5 39.5 + - - -
46H LEU* 4.8 3.1 - - + -
47H PHE* 3.7 36.3 - + + -
93H TYR* 3.9 0.6 - - - +
94H ASP* 1.3 79.7 - - - +
96H VAL* 1.3 64.3 + - - +
97H MET* 3.4 40.4 - - + -
121H LEU* 5.1 0.3 - - - +
142H LEU* 5.8 0.2 - - + -
143H LEU* 3.8 0.2 - - - -
144H ILE* 2.9 41.0 + - + +
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Residues in contact with VAL 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A ILE* 3.5 5.4 - - - +
720A PHE* 3.3 48.3 + - + -
721A LYS* 3.7 22.9 + - + +
63H LEU* 5.8 2.9 - - + -
90H ALA* 3.6 25.6 - - + +
93H TYR* 4.8 4.5 - - + -
95H TYR* 1.3 83.5 - - - +
97H MET* 1.3 71.8 + - - +
141H TYR* 6.2 1.3 - - + -
142H LEU 3.3 6.5 - - - +
143H LEU* 3.6 31.2 - - + -
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Residues in contact with MET 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718A THR* 3.3 17.7 - - - +
719A ILE* 4.0 5.8 - - + -
720A PHE* 4.0 7.8 - - - -
40H LEU* 4.5 9.2 - - + -
42H ILE* 4.5 8.3 - - + -
95H TYR* 3.4 38.8 - - + +
96H VAL* 1.3 79.9 - - - +
98H TYR* 1.3 64.5 + - - +
118H PHE* 3.4 47.6 - - + -
121H LEU* 3.8 17.7 - - + -
141H TYR* 3.6 10.0 - - - +
142H LEU* 2.9 41.7 + - + +
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Residues in contact with TYR 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A PRO* 3.9 39.9 - - + +
717A PRO 4.0 8.5 - - - +
718A THR* 3.3 10.5 + - - +
720A PHE* 3.5 17.9 - - + -
97H MET* 1.3 81.1 - - - +
99H GLY* 1.3 80.0 + - - +
100H THR* 4.3 3.5 + - - -
118H PHE* 3.2 20.2 - - - +
138H GLU* 3.3 8.1 + - - +
139H ASN* 2.6 39.5 + - - -
140H ALA 4.0 9.2 - - - -
141H TYR* 3.4 23.1 - + + -
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Residues in contact with GLY 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H TYR* 1.3 89.4 - - - +
100H THR* 1.3 69.6 + - - -
116H TYR* 5.3 2.7 - - - -
117H SER 3.3 16.4 - - - -
118H PHE* 3.4 11.4 - - - -
119H GLY 5.1 0.2 - - - -
138H GLU 3.2 11.8 - - - +
140H ALA* 3.6 16.3 + - - -
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Residues in contact with THR 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A LYS* 5.2 9.6 - - + -
777A LEU* 4.5 19.0 - - + +
98H TYR* 4.3 5.2 + - - -
99H GLY* 1.3 81.5 + - - -
101H ALA* 1.3 75.6 + - - +
102H TYR* 3.7 5.7 + - - -
116H TYR* 3.3 19.3 - - - +
117H SER 3.3 13.2 + - - +
137H GLN 4.0 12.3 - - - +
138H GLU* 3.1 21.7 + - + +
140H ALA* 5.5 1.8 - - - -
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Residues in contact with ALA 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A LYS* 3.7 14.7 - - - -
100H THR* 1.3 80.8 - - - +
102H TYR* 1.3 59.8 + - - +
104H PHE* 4.7 11.7 - - + -
115H TYR 5.0 0.9 - - - +
116H TYR* 3.5 18.9 - - + +
135H LEU 3.6 23.3 - - - +
136H LYS* 4.0 22.6 - - + +
137H GLN 3.7 7.0 + - - +
140H ALA* 5.7 1.2 - - - +
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Residues in contact with TYR 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A GLU* 5.8 0.2 + - - -
770A LEU* 4.1 23.9 - - + +
772A LYS* 3.6 32.2 + - + +
777A LEU* 3.7 27.4 - - + -
778A CYS* 4.9 6.0 - - + +
100H THR 4.0 2.5 - - - -
101H ALA* 1.3 73.5 - - - +
103H LYS* 1.3 96.5 - - + +
115H TYR* 3.5 17.1 + - + +
116H TYR* 3.6 28.9 - - - -
117H SER* 4.1 8.1 - - - -
122H LEU* 3.3 22.9 - - + +
136H LYS* 4.0 7.0 + - - +
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Residues in contact with LYS 103 (chain H).
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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768A GLU* 5.7 4.9 - - - -
770A LEU* 3.6 30.2 - - - +
102H TYR* 1.3 102.8 - - + +
104H PHE* 1.3 72.4 + - - +
115H TYR* 2.9 58.8 + - + +
136H LYS* 3.5 4.9 - - - +
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Residues in contact with PHE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ALA* 4.7 7.9 - - + -
103H LYS* 1.3 83.8 - - - +
105H GLU* 1.3 60.9 + - - +
106H GLU* 2.8 26.5 - - - +
112H ILE* 5.7 6.1 - - + -
113H ALA 4.0 2.2 - - - +
114H VAL* 3.5 29.4 - - + -
134H ASN* 3.2 28.9 - - + -
135H LEU* 3.5 30.1 - - + -
136H LYS* 3.4 37.6 - - + +
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Residues in contact with GLU 105 (chain H).
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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103H LYS 4.1 1.6 - - - -
104H PHE* 1.3 74.1 - - - +
106H GLU* 1.3 79.2 + - - +
107H VAL* 3.8 4.7 - - + +
112H ILE* 4.0 6.1 - - - +
113H ALA* 2.7 48.9 + - + +
115H TYR* 3.8 40.1 - - + +
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Residues in contact with GLU 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H PHE* 2.8 32.7 - - - +
105H GLU* 1.3 88.1 - - - +
107H VAL* 1.3 67.0 + - - +
111H LEU 4.5 2.2 - - - -
112H ILE* 5.2 11.0 - - + +
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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