Contacts of the strand formed by residues 114 - 122 (chain D) in PDB entry 4OZH
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 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103D PRO* 3.6 5.7 - - - +
104D SER* 2.9 51.7 + - - +
112D HIS* 5.3 0.9 - - - +
113D ASN* 1.3 102.5 + - - +
115D LEU* 1.3 61.5 + - - +
116D VAL* 4.2 0.9 - - + +
143D VAL* 5.5 3.8 - - + -
160D MET* 3.8 33.9 - - + -
161D LEU 3.5 9.0 - - - +
162D GLU* 5.1 5.8 - - + +
163D MET* 5.3 0.2 - - - +
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ILE* 3.8 12.3 - - + -
102D SER 4.3 1.3 - - - -
103D PRO* 4.3 11.7 - - + -
112D HIS* 6.4 0.7 - - + -
114D LEU* 1.3 78.0 - - - +
116D VAL* 1.3 58.1 + - - +
131D TRP* 3.7 28.6 - - + -
159D VAL 3.6 2.4 - - - +
160D MET* 3.5 1.7 - - - -
161D LEU* 2.8 53.8 + - + +
163D MET* 4.0 23.3 - - + -
171D TYR* 4.5 5.2 - - + -
188D TRP* 3.7 57.7 - - + -
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Residues in contact with VAL 116 (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 THR 3.7 1.7 - - - +
101D ILE* 3.3 23.2 - - - +
102D SER* 3.4 31.7 + - - +
104D SER* 5.1 11.2 - - - -
114D LEU* 4.2 0.8 - - + -
115D LEU* 1.3 74.3 - - - +
117D CYS* 1.3 61.7 + - - +
118D SER* 4.2 6.5 - - - +
131D TRP* 4.4 1.6 - - - -
158D LEU* 3.8 30.5 - - + -
159D VAL 3.4 8.1 - - - +
160D MET* 3.8 39.3 - - + +
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Residues in contact with CYS 117 (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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99D VAL* 4.6 20.4 - - - -
100D THR 3.8 2.7 - - - -
101D ILE* 3.9 12.1 - - - -
116D VAL* 1.3 71.6 - - - +
118D SER* 1.3 59.5 + - - +
119D VAL* 3.2 17.9 + - - +
129D VAL* 5.0 0.4 - - + -
131D TRP* 3.6 16.5 - - + +
157D ILE 3.8 0.7 - - - +
159D VAL* 3.0 30.5 + - + +
173D CYS* 2.0 50.9 - - - -
186D VAL* 5.8 0.4 - - - -
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Residues in contact with SER 118 (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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96C PRO* 3.9 28.4 - - - +
98D THR 3.0 15.8 - - - +
99D VAL* 3.4 1.2 - - - -
100D THR* 2.8 31.5 + - - -
102D SER* 4.7 4.5 + - - -
116D VAL* 3.7 11.5 - - - +
117D CYS* 1.3 68.0 - - - +
119D VAL* 1.3 60.0 + - - +
120D THR* 3.7 5.9 + - - -
158D LEU* 3.4 29.7 - - - +
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Residues in contact with VAL 119 (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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97D PRO* 3.8 14.6 - - + -
98D THR 3.7 2.9 - - - -
99D VAL* 3.8 22.2 - - + -
117D CYS* 3.5 14.6 - - - +
118D SER* 1.3 69.6 - - - +
120D THR* 1.3 62.5 + - - +
122D PHE* 3.7 18.4 - - + -
127D ILE* 3.8 17.9 - - + -
129D VAL* 4.3 12.3 - - + -
156D GLN* 3.3 1.9 - - - -
157D ILE* 2.9 53.5 + - + +
159D VAL* 5.4 0.9 - - + -
175D VAL* 4.1 14.8 - - + -
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Residues in contact with THR 120 (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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94C LYS 3.4 20.0 - - - +
95C SER* 4.0 12.7 - - - -
96C PRO* 4.2 17.1 - - + +
97D PRO* 3.6 1.2 - - - +
98D THR* 2.8 48.4 + - - +
118D SER* 4.3 9.1 + - - -
119D VAL* 1.3 79.0 - - - +
121D ASP* 1.4 79.6 + - - +
122D PHE* 4.1 2.7 - - - -
155D PHE 3.9 1.3 - - - -
156D GLN* 3.5 19.7 - - - +
157D ILE 6.2 0.2 - - - -
158D LEU* 5.9 2.9 - - + -
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Residues in contact with ASP 121 (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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94C LYS* 2.7 46.0 + - - +
95C SER* 4.5 7.1 - - - -
95D VAL* 3.7 9.3 - - + +
96D GLU 3.0 21.1 - - - +
97D PRO* 3.4 0.2 - - - +
98D THR* 5.0 6.7 + - - +
120D THR* 1.4 90.9 + - - +
122D PHE* 1.4 58.8 + - - +
150D ASN* 5.1 2.1 + - - +
154D THR* 3.8 20.8 + - + +
155D PHE 3.0 12.3 + - - -
156D GLN* 4.4 1.4 - - - +
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Residues in contact with PHE 122 (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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95D VAL* 3.6 15.3 - - - +
97D PRO* 3.8 25.8 - - + -
119D VAL* 3.7 20.9 - - + -
120D THR 4.1 2.7 - - - -
121D ASP* 1.4 74.8 - - - +
123D TYR* 1.3 60.7 + - - +
124D PRO 3.7 7.4 - - - -
125D ALA 4.2 4.5 - - - -
127D ILE* 3.6 34.1 - - + -
147D LEU* 4.3 4.5 - - + -
154D THR* 3.6 4.1 - - - -
155D PHE* 2.9 74.6 + - + +
156D GLN* 3.8 9.4 - - - -
157D ILE* 4.1 10.5 - - + -
177D HIS* 3.4 27.1 - + + +
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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