Contacts of the strand formed by residues 109 - 117 (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 LYS 109 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I THR* 4.0 0.4 - - - -
102I THR* 2.7 56.7 + - + +
108I GLY* 1.3 71.5 - - - -
110I PRO* 1.3 90.2 + - + +
111I ILE* 5.6 0.4 - - - +
52T ALA* 4.9 15.8 - - - +
55T TRP* 3.3 45.6 - - + -
56T GLU* 5.6 5.4 - - - -
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Residues in contact with PRO 110 (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* 4.1 12.1 - - + -
99I GLU* 3.3 29.6 - - - +
100I GLY 3.2 9.6 - - - +
101I THR* 4.3 2.5 - - + -
108I GLY 3.5 6.7 - - - +
109I LYS* 1.3 110.9 + - + +
111I ILE* 1.3 60.8 + - - +
51T THR* 3.7 31.6 - - - +
52T ALA* 3.9 7.4 - - + +
55T TRP* 3.8 15.9 - - + -
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Residues in contact with ILE 111 (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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100I GLY* 2.9 33.5 + - - +
101I THR 4.2 3.4 - - - +
102I THR* 3.5 37.5 - - + +
109I LYS* 4.0 2.7 - - - +
110I PRO* 1.3 74.6 - - - +
112I GLY* 1.3 58.9 + - - +
113I ALA* 3.0 11.7 + - + +
115I ALA* 5.0 0.7 - - + -
33M LYS* 5.2 2.6 - - - +
47M LEU* 3.8 21.5 - - + -
50M TYR* 3.4 52.1 - - + -
56M PRO* 5.3 2.2 - - + -
92M TYR* 3.5 18.0 + - - -
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Residues in contact with GLY 112 (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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33I ALA* 5.7 1.1 - - - +
99I GLU* 2.9 31.1 + - - +
110I PRO 3.7 0.6 - - - -
111I ILE* 1.3 73.7 - - - +
113I ALA* 1.3 67.0 + - - +
114I PHE* 3.4 16.3 - - - -
92M TYR* 4.1 15.0 - - - -
48T PHE* 4.7 19.3 + - - -
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Residues in contact with ALA 113 (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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99I GLU* 3.3 0.2 - - - -
100I GLY 3.1 21.0 + - - -
111I ILE* 3.0 13.8 + - + +
112I GLY* 1.3 75.7 - - - +
114I PHE* 1.3 62.5 + - - +
115I ALA 3.5 0.3 + - - -
35M ALA* 3.7 15.3 - - + -
37M TYR* 3.6 12.3 - - - +
47M LEU* 3.7 23.8 - - + -
50M TYR* 3.8 16.4 - - + -
90M GLN* 4.5 3.6 - - - -
92M TYR* 3.8 10.6 - - + +
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Residues in contact with PHE 114 (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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33I ALA* 5.7 4.0 - - + -
35I SER* 4.0 26.0 - - - -
37I VAL* 4.2 11.2 - - + -
47I TRP* 4.0 10.3 - + - -
97I ALA* 3.6 28.7 - - + -
98I ARG 3.7 7.4 - - - +
99I GLU* 4.6 8.7 - - + -
112I GLY 3.4 18.2 - - - -
113I ALA* 1.3 68.9 - - - +
115I ALA* 1.3 60.1 + - - +
116I HIS 3.4 0.4 - - - -
117I TRP* 2.9 37.4 + + + +
37M TYR* 3.0 29.0 + + - +
47M LEU* 3.5 6.3 - - - +
90M GLN* 3.1 32.1 - - - -
92M TYR* 6.3 0.2 - - + -
99M PHE* 4.1 9.2 - + - -
48T PHE* 4.3 10.8 - + - -
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Residues in contact with ALA 115 (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 3.4 3.8 + - - -
100I GLY* 3.8 23.1 - - - +
111I ILE* 5.0 1.1 - - + -
113I ALA 3.5 3.6 + - - -
114I PHE* 1.3 73.8 - - - +
116I HIS* 1.3 74.4 + - + +
117I TRP* 4.0 6.6 + - - -
46M ARG* 5.7 1.6 - - - +
47M LEU* 3.9 27.2 + - + +
56M PRO* 5.9 3.6 - - + -
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Residues in contact with HIS 116 (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* 3.8 50.2 + - + +
4I LEU* 3.7 7.7 - - + +
97I ALA* 3.3 4.7 - - - +
98I ARG* 2.8 55.8 + - + +
99I GLU 3.7 13.2 + - - -
100I GLY* 4.0 8.3 - - - -
101I THR* 5.0 5.3 + - - -
114I PHE 3.4 0.4 - - - -
115I ALA* 1.3 95.3 + - + +
117I TRP* 1.3 62.9 + - - +
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Residues in contact with TRP 117 (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* 4.0 15.5 + - - +
37I VAL* 4.1 22.7 - - + -
45I LEU* 4.7 1.6 - - + -
95I TYR* 3.7 31.4 - + + -
96I CYS 3.7 3.1 - - - -
97I ALA* 3.8 12.1 - - + -
114I PHE* 2.9 52.6 + + + -
115I ALA 4.0 5.1 + - - -
116I HIS* 1.3 82.8 - - - +
118I GLY* 1.3 69.3 + - - +
37M TYR* 3.8 18.3 - + - -
44M ALA* 4.1 9.6 - - + -
45M PRO* 3.2 55.6 + - + +
46M ARG* 4.8 2.2 - - - +
99M PHE* 4.5 7.2 - + - -
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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