Contacts of the strand formed by residues 92 - 102 (chain I) in PDB entry 3H3P
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 92 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ARG* 4.0 15.3 - - - -
39I GLN 3.2 21.1 - - - +
40I ALA* 3.9 5.2 - - + +
41I PRO* 4.2 4.5 - - - -
90I ASP 3.2 10.0 + - - +
91I THR* 1.3 80.4 - - - +
93I VAL* 1.3 66.4 + - - +
94I TYR* 3.6 12.4 - - + -
122I LEU* 3.1 9.0 - - - +
123I VAL 2.9 30.0 + - - +
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Residues in contact with VAL 93 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I VAL 4.2 0.2 - - - +
38I ARG* 3.4 2.6 - - - -
39I GLN* 2.7 40.3 + - + +
41I PRO* 5.3 1.1 - - + +
92I ALA* 1.3 75.7 - - - +
94I TYR* 1.3 63.4 + - - +
95I TYR* 3.7 34.9 + - + +
119I GLN 5.0 1.1 - - - +
120I GLY* 3.8 19.1 - - - -
121I THR 3.6 7.4 - - - +
122I LEU* 3.9 24.5 - - + +
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Residues in contact with TYR 94 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 2.8 23.7 + - - -
20I VAL* 5.2 4.0 - - + -
36I TRP* 4.1 4.6 - + + -
37I VAL 3.7 2.7 - - - -
38I ARG* 3.1 32.0 + - + -
48I MET* 3.6 35.7 - - + -
81I LEU* 4.0 20.0 - - + -
83I LEU* 3.4 30.5 - - + +
90I ASP* 2.5 31.9 + - - +
92I ALA* 3.6 20.6 - - + -
93I VAL* 1.3 73.2 - - - +
95I TYR* 1.3 62.3 + - - +
121I THR* 3.0 21.5 + - - +
123I VAL* 3.8 24.0 - - + -
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Residues in contact with TYR 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 3.4 2.7 - - - -
36I TRP* 3.4 9.1 - - - -
37I VAL* 2.7 44.9 + - + +
39I GLN* 3.6 26.3 + - + -
45I LEU* 4.4 9.4 - - + -
93I VAL* 3.7 23.6 - - + +
94I TYR* 1.3 74.1 - - - +
96I CYS* 1.3 59.3 + - - +
117I TRP* 3.7 31.0 - + + -
118I GLY 3.8 12.6 - - - -
119I GLN 3.7 18.3 + - - -
120I GLY* 3.8 13.0 - - - -
39M GLN* 3.5 21.1 + - - -
42M GLY 5.4 2.3 - - - -
43M GLN 3.7 8.0 + - - -
44M ALA* 3.9 19.7 - - + -
45M PRO* 4.2 1.3 - - + -
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Residues in contact with CYS 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 3.8 12.6 - - + -
6I GLN* 3.0 24.0 + - - -
22I CYS* 2.1 54.7 - - + -
34I LEU* 4.6 4.5 - - + -
35I SER 3.1 10.1 - - - +
36I TRP* 3.8 14.4 - - + -
95I TYR* 1.3 77.3 - - - +
97I ALA* 1.3 62.8 + - - +
117I TRP* 3.7 1.2 - - - -
118I GLY 3.0 25.7 + - - -
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Residues in contact with ALA 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I LEU* 3.9 3.8 - - - -
33I ALA 4.0 0.5 - - - +
34I LEU* 3.5 2.6 - - - +
35I SER* 2.7 42.1 + - - +
37I VAL* 5.3 2.5 - - + -
96I CYS* 1.3 77.1 - - - +
98I ARG* 1.3 60.1 + - - +
114I PHE* 3.6 34.8 - - + -
116I HIS 3.3 8.5 - - - +
117I TRP* 3.8 20.2 - - + -
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Residues in contact with ARG 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I VAL* 4.1 33.2 - - + +
4I LEU* 3.6 22.4 - - + +
27I GLY* 4.6 1.6 - - - -
28I SER 4.2 14.7 + - - +
29I PHE* 5.8 1.5 - - - +
32I TYR* 3.4 61.2 - - - +
33I ALA 3.5 9.0 - - - +
34I LEU* 4.5 9.2 - - + +
97I ALA* 1.3 75.1 - - - +
99I GLU* 1.3 94.9 + - - +
101I THR* 4.3 6.7 - - - +
106I TRP 4.6 8.7 + - - -
114I PHE* 3.7 3.8 - - - -
115I ALA 3.4 3.8 + - - -
116I HIS* 2.8 41.5 + - + +
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Residues in contact with GLU 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I TYR* 3.7 2.1 - - + -
33I ALA* 2.8 48.5 + - + +
98I ARG* 1.3 115.5 + - - +
100I GLY* 1.3 59.4 + - - +
110I PRO* 3.3 19.0 - - + +
112I GLY* 2.9 44.9 + - - +
113I ALA 3.3 7.9 - - - +
114I PHE* 4.2 3.2 - - + +
116I HIS* 3.7 1.3 - - - -
48T PHE 4.7 2.3 - - - +
51T THR* 2.5 30.6 + - - +
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Residues in contact with GLY 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I ARG 3.7 1.0 + - - -
99I GLU* 1.3 76.0 - - - +
101I THR* 1.3 63.7 + - - +
110I PRO* 3.2 8.0 - - - +
111I ILE* 2.9 33.8 + - - +
113I ALA 3.1 12.9 + - - -
115I ALA* 3.8 21.9 - - - +
116I HIS* 4.0 7.4 - - - -
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Residues in contact with THR 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I TYR* 3.3 38.1 - - + +
98I ARG* 4.3 6.5 - - - +
100I GLY* 1.3 78.0 - - - +
102I THR* 1.3 65.2 + - - +
103I GLY 3.4 10.4 + - - +
106I TRP* 4.0 22.4 + - - +
108I GLY* 3.4 23.6 - - - +
109I LYS 3.2 5.2 - - - +
111I ILE* 4.2 6.2 - - - +
116I HIS* 5.0 5.6 + - - +
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Residues in contact with THR 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I THR* 1.3 68.8 - - - +
103I GLY* 1.3 58.8 + - - +
108I GLY* 3.9 15.0 - - - -
109I LYS* 2.7 43.8 + - + +
110I PRO 5.3 0.4 - - - +
111I ILE* 3.5 23.3 - - + -
50M TYR* 3.6 16.8 - - + +
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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