Contacts of the strand formed by residues 43 - 49 (chain A) 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 GLY 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ASP* 1.3 76.5 - - - +
44A LEU* 1.3 67.2 + - - -
45A TRP* 3.6 4.0 - - - -
78A PRO* 3.5 1.7 - - - +
79A VAL 2.9 35.1 + - - -
103A ARG* 3.7 1.8 - - - -
363D TRP* 3.6 34.4 - - - +
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Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLY* 1.3 72.8 - - - -
45A TRP* 1.3 61.4 + - - +
76A ASP* 4.1 20.6 - - + +
77A MET 3.9 1.6 - - - -
78A PRO* 4.8 5.2 - - + -
103A ARG* 3.1 23.0 + - - +
363D TRP* 3.6 31.2 - - + -
367D VAL* 3.5 32.3 - - + -
395D MET* 3.9 14.8 - - + -
398D ARG* 3.8 25.8 - - - +
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Residues in contact with TRP 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.0 34.6 + - + -
43A GLY 3.6 3.1 - - - -
44A LEU* 1.3 83.7 - - - +
46A SER* 1.3 66.5 + - - +
76A ASP* 3.5 6.3 - - - -
77A MET* 2.8 38.3 + - - +
79A VAL* 3.4 30.4 - - + +
101A TYR* 3.8 18.4 - - + -
102A GLU* 3.5 27.1 - - - +
103A ARG* 3.6 29.6 - - + +
168A ILE* 4.0 17.7 - - + -
170A ILE* 4.0 29.6 - - + -
214A LEU* 4.1 3.6 - - + -
218A VAL* 4.1 27.1 - - + -
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 1.3 75.0 - - - +
47A PHE* 1.3 59.2 + - - +
68A LEU* 4.4 9.0 - - - -
69A TRP* 5.9 1.6 - - - -
74A THR* 4.5 16.8 + - - -
75A VAL 3.6 5.6 - - - -
76A ASP* 5.0 3.3 + - - +
101A TYR* 3.3 6.2 - - - -
102A GLU* 2.9 46.2 + - - -
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A SER* 1.3 77.5 - - - +
48A ARG* 1.3 61.8 + - - +
49A ALA* 3.9 14.6 - - + -
68A LEU* 4.4 2.0 - - - +
74A THR* 3.3 8.1 - - - -
75A VAL* 2.9 54.4 + - + +
77A MET* 3.5 28.7 - - + -
83A PHE* 3.9 22.4 - + + -
92A LEU* 4.1 20.0 - - + -
99A VAL* 3.8 30.3 - - + -
100A TRP 3.2 10.8 - - - -
101A TYR* 3.6 43.7 - + + -
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Residues in contact with ARG 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 1.3 83.1 - - - +
49A ALA* 1.3 72.2 + - - +
57A ARG* 5.3 11.3 - - - +
63A TRP* 3.0 51.0 - - + -
68A LEU* 4.3 10.4 + - + +
71A SER* 3.0 30.4 + - - -
72A GLY* 3.6 6.7 - - - -
73A PRO* 3.4 42.6 + - - +
74A THR* 4.4 7.6 - - + -
75A VAL* 5.6 0.2 - - - -
99A VAL* 3.7 0.3 - - - -
100A TRP* 2.8 36.1 + - + +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PHE* 3.9 5.2 - - + -
48A ARG* 1.3 90.9 + - - +
50A ASP* 1.3 60.3 + - - +
51A PHE* 3.4 42.6 + - + -
92A LEU* 3.9 20.4 - - + -
95A PHE* 4.3 7.6 - - + -
98A TRP 3.9 4.7 - - - -
99A VAL* 4.1 13.2 - - + -
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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