Contacts of the strand formed by residues 98 - 105 (chain D) in PDB entry 3HN3
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 TRP 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D ASP* 3.1 28.9 + - + +
55D ARG* 3.2 29.7 + - + +
56D ARG* 5.2 4.8 - - - +
59D PHE* 3.5 28.5 - + + -
95D PHE* 3.4 6.1 - - - -
97D GLY* 1.3 72.3 - - - -
99D VAL* 1.3 61.9 + - - +
100D TRP* 3.8 16.9 - - + +
129D TYR* 4.0 18.4 - + + -
131D ILE* 3.8 23.6 - - + -
171D ALA* 3.6 33.0 - - + -
172D ILE 3.3 9.4 - - - -
173D ASN* 3.1 49.3 - - + +
1G NAG 3.6 20.5 + - + -
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Residues in contact with VAL 99 (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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47D PHE* 3.7 20.6 - - + -
48D ARG 3.7 3.8 - - - +
49D ALA* 4.1 6.1 - - + -
83D PHE* 3.8 31.0 - - + -
95D PHE* 3.6 29.2 - - + -
97D GLY 5.3 0.7 - - - +
98D TRP* 1.3 73.1 - - - +
100D TRP* 1.3 61.8 + - - +
101D TYR* 3.8 24.0 - - + -
170D ILE 3.7 1.2 - - - +
171D ALA* 3.3 3.8 - - - -
172D ILE* 2.9 51.2 + - + +
174D ASN* 5.9 0.4 - - - +
213D GLY* 5.3 0.2 - - - -
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Residues in contact with TRP 100 (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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46D SER 3.7 0.2 - - - +
47D PHE* 3.2 7.6 - - - -
48D ARG 2.8 41.7 + - - +
50D ASP* 4.1 6.6 + - + +
58D GLY* 3.8 28.3 - - - -
59D PHE* 3.7 26.9 - + - -
63D TRP* 3.7 37.3 - + + -
64D TYR* 4.1 25.1 - + + -
68D LEU* 3.7 19.3 - - + +
98D TRP* 3.8 22.5 - - - +
99D VAL* 1.3 80.3 - - - +
101D TYR* 1.3 63.2 + - - +
133D TRP* 3.7 31.4 - + - -
169D THR* 4.1 16.8 - - + -
170D ILE 3.6 3.6 - - - -
171D ALA* 4.0 11.7 - - + -
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Residues in contact with TYR 101 (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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45D TRP* 4.0 27.1 - - + -
46D SER 3.2 6.1 - - - -
47D PHE* 3.6 26.2 - + - -
68D LEU* 4.6 1.3 - - - -
77D MET* 3.6 30.3 - - + +
78D PRO 4.8 0.6 + - - -
79D VAL* 4.0 14.8 - - + -
81D SER 4.2 4.0 + - - -
83D PHE* 3.9 5.0 - - - +
99D VAL* 3.8 15.5 - - + -
100D TRP* 1.3 77.9 - - - +
102D GLU* 1.3 63.5 + - - +
169D THR* 3.4 5.5 - - - +
170D ILE* 2.8 38.1 + - + +
172D ILE* 4.0 25.8 - - + -
213D GLY* 3.2 21.5 - - - -
214D LEU* 3.4 25.0 + - + -
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Residues in contact with GLU 102 (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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45D TRP* 3.5 8.3 - - - -
46D SER* 2.7 46.1 + - - +
63D TRP 5.4 0.2 - - - +
66D ARG 4.0 0.7 - - - +
67D PRO* 3.3 8.1 - - - +
68D LEU* 2.8 45.4 + - + +
69D TRP* 5.7 0.2 - - - -
101D TYR* 1.3 78.1 - - - +
103D ARG* 1.3 65.5 + - - +
104D GLU* 5.1 4.9 - - + +
167D ARG* 3.0 33.2 + - + -
168D ILE 3.2 13.2 - - - +
169D THR* 2.9 24.5 + - + +
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Residues in contact with ARG 103 (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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32A GLU* 5.9 1.2 + - - -
40A GLU* 5.5 3.4 + - - -
40D GLU 4.4 3.2 + - - -
41D LEU* 3.6 37.1 + - + +
42D ASP 3.1 29.0 + - - -
43D GLY* 3.8 0.8 - - - -
44D LEU 3.1 33.5 + - - +
45D TRP* 3.5 35.1 - - + +
102D GLU* 1.3 75.9 - - - +
104D GLU* 1.3 79.8 + - - +
105D VAL* 4.1 11.1 - - + +
166D LEU 3.8 0.5 - - - +
167D ARG* 3.6 1.4 - - - -
168D ILE* 2.8 34.4 + - + +
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Residues in contact with GLU 104 (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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67D PRO* 4.8 12.0 - - - +
69D TRP* 6.1 0.3 - - - -
102D GLU* 5.1 6.1 - - + +
103D ARG* 1.3 91.4 + - - +
105D VAL* 1.3 63.2 + - - +
165D ARG* 3.2 51.3 + - - +
166D LEU 3.3 4.9 - - - +
167D ARG* 4.0 32.5 - - + +
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Residues in contact with VAL 105 (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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32A GLU* 6.0 0.9 - - - -
39D LYS* 3.8 20.9 - - - -
41D LEU* 3.7 26.5 - - + -
103D ARG* 4.1 17.0 - - + +
104D GLU* 1.3 79.2 - - - +
106D ILE* 1.3 64.7 + - - +
107D LEU* 3.9 19.3 + - + -
165D ARG* 3.6 4.9 - - - -
166D LEU* 2.7 46.3 + - + +
168D ILE* 4.1 20.9 - - + -
220D LEU* 4.2 2.9 - - + -
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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