Contacts of the strand formed by residues 91 - 98 (chain D) in PDB entry 4PP8
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 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D THR* 5.1 5.6 - - + -
11D ILE 3.4 11.2 - - - +
12D LYS* 4.4 4.0 - - + +
76D VAL* 6.1 1.6 - - - -
89D TYR* 2.6 45.4 + + + +
90D PRO* 1.3 76.4 - - - +
92D LEU* 1.3 58.4 + - - +
93D GLN* 3.1 42.6 + - + -
113D ASN 3.8 0.2 - - - +
114D ILE* 4.0 1.0 - - - -
115D SER* 2.7 53.4 + - - -
116D ASP* 3.2 27.5 + - - -
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Residues in contact with LEU 92 (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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9D LEU 3.8 0.5 - - - +
10D THR* 3.3 6.1 - - - +
11D ILE* 2.8 43.8 + - + +
72D LEU* 3.9 25.6 - - + -
76D VAL* 3.6 32.9 - - + +
91D HIS* 1.3 73.5 - - - +
93D GLN* 1.3 70.5 + - - +
94D VAL* 3.9 21.3 - - + -
112D PHE* 4.7 4.3 - - + -
113D ASN 3.5 19.5 - - - +
114D ILE* 3.8 23.1 - - + +
143D TRP* 4.0 13.5 - - + -
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Residues in contact with GLN 93 (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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9D LEU 3.3 6.7 - - - +
10D THR* 4.7 11.7 - - + +
91D HIS* 3.1 36.3 + - + +
92D LEU* 1.3 76.4 - - - +
94D VAL* 1.3 64.5 + - - +
95D THR* 5.4 2.5 - - - +
111D GLU 3.9 0.7 - - - +
112D PHE* 3.7 0.2 - - - -
113D ASN* 2.6 79.9 + - + +
116D ASP* 3.8 5.1 + - - -
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Residues in contact with VAL 94 (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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7D CYS 3.6 1.4 - - - +
8D ASN* 3.4 3.6 - - - +
9D LEU* 2.7 53.2 + - + +
11D ILE* 5.3 0.7 - - + -
68D LEU* 5.8 0.2 - - + -
72D LEU* 4.0 16.4 - - + -
92D LEU* 3.9 17.5 - - + -
93D GLN* 1.3 79.2 - - - +
95D THR* 1.3 64.5 + - - +
110D TRP* 3.7 33.9 - - + -
111D GLU 3.2 10.5 - - - +
112D PHE* 3.7 30.7 - - + -
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Residues in contact with THR 95 (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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6D ARG* 3.7 22.4 - - + +
7D CYS 3.4 2.0 - - - -
8D ASN* 3.4 26.0 + - - +
93D GLN* 5.4 3.1 - - - +
94D VAL* 1.3 77.0 - - - +
96D MET* 1.3 63.1 + - - +
97D ILE* 3.9 12.2 - - + +
109D THR 3.4 1.9 - - - +
110D TRP* 3.4 2.9 - - - -
111D GLU* 2.7 60.9 + - - +
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Residues in contact with MET 96 (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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5D LEU* 3.7 13.3 - - + +
6D ARG* 3.2 7.1 - - - +
7D CYS* 2.8 62.4 + - + +
9D LEU* 5.3 0.6 - - + +
61D LEU* 5.1 1.8 - - + -
65D LEU* 5.8 1.3 - - + -
94D VAL 4.1 0.6 - - - -
95D THR* 1.3 72.7 - - - +
97D ILE* 1.3 68.1 + - - +
98D TYR* 3.8 22.7 - - - -
108D ALA* 4.1 1.6 - - + -
109D THR 3.3 5.4 - - - +
110D TRP* 3.6 45.5 - - + +
156D LEU* 4.2 21.1 - - + -
157D ILE* 3.9 11.2 - - + -
164D MET* 4.4 8.3 - - - -
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Residues in contact with ILE 97 (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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4D SER* 3.8 24.0 - - - +
5D LEU 3.6 2.7 - - - -
6D ARG* 3.3 37.2 - - + +
95D THR* 3.9 11.0 - - + +
96D MET* 1.3 78.8 - - - +
98D TYR* 1.3 61.6 + - - +
99D PRO* 3.7 7.7 - - + +
108D ALA* 3.3 5.0 - - - -
109D THR* 2.9 46.0 + - + +
111D GLU* 4.0 26.0 - - - +
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Residues in contact with TYR 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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4D SER* 3.6 3.5 - - - -
5D LEU* 2.8 39.7 + - + +
96D MET* 3.8 16.4 - - - -
97D ILE* 1.3 73.8 - - - +
99D PRO* 1.3 74.0 - - - +
101D SER* 2.7 14.7 + - - -
106D PRO* 4.0 6.5 - - + -
107D SER 3.2 28.3 - - - -
108D ALA* 4.3 1.1 - - + -
157D ILE* 3.8 22.9 - - + -
161D SER* 3.4 13.8 + - - -
164D MET* 3.6 49.4 - - + -
165D ASP* 2.6 32.6 + - - -
168D LEU* 4.0 8.6 - - + +
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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