Contacts of the strand formed by residues 89 - 95 (chain B) in PDB entry 4ZM9
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 ALA 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B ILE 3.3 11.9 - - - +
82B MET* 4.2 4.0 - - + -
87B LEU 4.0 4.7 - - - +
88B SER* 1.3 79.9 - - - +
90B GLY* 1.3 58.4 + - - +
109B MET* 3.6 17.4 - - - +
115B CYS* 3.5 20.0 - - + +
203B LEU* 3.6 36.3 - - + -
404B BME 3.4 19.9 - - - -
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B SER* 3.1 3.6 - - - -
81B ILE* 3.0 33.1 + - - +
89B ALA* 1.3 76.1 - - - +
91B ALA* 1.3 61.4 + - - +
105B ALA* 3.3 26.6 - - - +
108B VAL* 4.2 0.9 - - - -
109B MET* 3.8 10.1 - - - +
115B CYS 3.2 7.6 - - - -
203B LEU* 5.8 0.2 - - - -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA 3.0 14.4 - - - +
80B SER* 3.5 4.7 - - - -
90B GLY* 1.3 77.1 - - - +
92B VAL* 1.3 68.8 + - - +
105B ALA* 4.0 5.7 + - - +
108B VAL* 4.0 4.1 - - - +
115B CYS 2.8 13.1 + - - +
116B PHE* 3.3 12.4 - - + -
117B LEU 3.0 22.3 + - - -
201B PRO* 3.3 26.2 - - + +
203B LEU* 5.3 3.4 - - + -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASP* 3.2 3.0 - - - -
79B ALA* 2.9 43.4 + - + +
91B ALA* 1.3 80.5 - - - +
93B SER* 1.3 60.0 + - - +
95B VAL* 4.0 29.2 - - + -
101B PRO* 3.9 21.3 - - + +
104B LEU* 3.9 27.1 - - + -
105B ALA 4.3 4.3 - - - +
108B VAL* 4.0 15.3 - - + -
116B PHE* 4.0 3.8 - - - -
117B LEU* 3.1 11.2 - - + +
122B ALA* 4.5 5.8 - - + -
201B PRO* 3.5 4.3 - - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 5.0 1.4 + - - -
116A PHE* 6.0 0.2 - - - -
118A THR* 4.5 0.7 + - - -
77B MET 3.9 0.4 - - - -
78B ASP* 3.2 10.8 - - - -
92B VAL* 1.3 75.4 - - - +
94B ALA* 1.3 63.9 + - - +
95B VAL* 3.4 5.6 + - - +
116B PHE* 3.4 18.7 - - - -
117B LEU 3.1 4.6 + - - -
118B THR* 2.6 30.5 + - - -
119B ASP 2.9 27.2 + - - -
197B VAL* 3.8 27.4 - - - +
201B PRO* 4.2 1.1 - - - -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A THR* 3.7 26.7 - - + -
76B GLU* 4.2 25.1 - - - +
77B MET 3.0 9.5 + - - +
78B ASP* 2.8 15.3 + - - -
93B SER* 1.3 74.6 - - - +
95B VAL* 1.3 62.0 + - - +
96B GLN* 4.6 4.5 - - - +
118B THR* 4.3 0.7 - - - +
119B ASP* 3.5 26.5 - - + +
195B GLY* 4.6 7.0 - - - -
196B ARG 5.1 3.1 - - - +
197B VAL* 5.1 1.6 - - + -
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLU* 3.5 5.0 - - - -
77B MET* 2.9 58.6 + - + +
92B VAL* 4.0 26.9 - - + -
93B SER 4.1 2.0 - - - +
94B ALA* 1.3 76.0 - - - +
96B GLN* 1.3 62.4 + - - +
98B ILE* 4.6 14.6 - - + -
101B PRO* 4.3 11.7 - - + -
104B LEU* 4.1 9.4 - - + -
119B ASP* 4.8 2.9 - - - +
122B ALA* 3.6 33.2 - - + -
123B ALA* 5.0 2.2 - - + +
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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