Contacts of the strand formed by residues 67 - 75 (chain D) in PDB entry 3HPN
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 ILE 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LEU* 4.2 16.2 - - + -
64D ALA* 4.0 20.6 - - + -
66D ARG* 1.3 79.0 - - - +
68D PHE* 1.3 61.7 + - - +
69D ILE* 4.3 16.3 + - + -
96D TYR* 6.3 1.6 - - + -
142D SER* 3.2 7.8 - - - -
143D VAL* 3.0 47.1 + - + +
146D LEU* 3.5 27.6 - - + -
151D PHE* 3.5 33.0 - - + -
153D LEU* 4.5 2.7 - - + -
169D VAL* 3.8 12.8 - - + -
170D TYR 3.4 7.0 - - - +
171D TYR* 4.3 2.5 - - + -
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Residues in contact with PHE 68 (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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66D ARG* 4.1 29.2 - - + -
67D ILE* 1.3 74.8 - - - +
69D ILE* 1.3 60.8 + - - +
70D GLU 4.1 0.4 - - - -
140D GLU* 3.9 18.2 - - - -
141D ARG 3.5 2.5 - - - -
142D SER* 3.8 21.1 - - - -
168D ARG 3.6 1.0 - - - +
169D VAL* 3.2 6.4 - - - +
170D TYR* 2.6 70.3 + + + +
171D TYR* 4.4 1.3 - - - -
172D LYS* 3.7 41.1 - - + -
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Residues in contact with ILE 69 (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 ILE* 4.4 13.0 - - + +
68D PHE* 1.3 78.0 - - - +
70D GLU* 1.3 60.8 + - - +
71D LEU* 4.0 24.5 - - + +
94D LEU* 4.3 15.0 - - + -
115D ILE* 4.0 9.4 - - + -
139D GLU 3.6 1.7 - - - +
140D GLU* 3.1 6.3 - - - +
141D ARG 2.7 40.7 + - - +
143D VAL* 3.7 28.9 - - + -
153D LEU* 3.8 44.2 - - + -
167D VAL* 4.9 0.9 - - + -
168D ARG 3.5 4.9 - - - +
169D VAL* 4.4 4.7 - - + -
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Residues in contact with GLU 70 (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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68D PHE 4.1 0.4 - - - -
69D ILE* 1.3 72.8 - - - +
71D LEU* 1.3 64.9 + - - +
72D LYS* 3.9 24.2 + - - +
138D VAL* 4.0 22.7 - - + +
139D GLU 3.6 3.4 - - - +
140D GLU* 3.9 20.1 - - + +
166D SER* 3.7 5.5 + - - +
167D VAL* 3.4 5.5 - - - -
168D ARG* 2.7 73.6 + - + +
170D TYR* 4.7 4.3 - - + -
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Residues in contact with LEU 71 (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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69D ILE* 4.0 12.6 - - + +
70D GLU* 1.3 80.6 - - - +
72D LYS* 1.3 63.7 + - - +
73D PHE* 4.0 13.8 - - + -
92D PHE* 4.2 9.9 - - + -
94D LEU* 4.3 10.1 - - + -
118D ILE* 4.1 33.4 - - + -
137D ASN 3.5 0.3 - - - +
138D VAL* 3.3 6.4 - - - +
139D GLU* 2.8 41.2 + - + +
141D ARG* 6.1 0.4 - - + -
155D PHE* 3.6 33.4 - - + -
164D LEU* 4.3 4.7 - - + -
166D SER 3.4 1.6 - - - +
167D VAL* 3.9 23.8 - - + -
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Residues in contact with LYS 72 (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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131C ALA* 2.8 40.4 + - - +
132C ARG* 4.3 4.7 - - + -
133C HIS* 5.2 6.1 - - - -
70D GLU* 3.9 27.4 + - + +
71D LEU* 1.3 77.5 - - - +
73D PHE* 1.3 59.1 + - - +
136D LEU* 4.1 17.7 - - + +
137D ASN 3.1 6.1 - - - +
138D VAL* 4.0 28.0 - - + -
164D LEU* 3.6 2.6 - - - +
165D LEU* 2.8 31.2 + - + -
166D SER* 2.9 34.3 + - - +
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Residues in contact with PHE 73 (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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71D LEU* 4.0 9.6 - - + -
72D LYS* 1.3 77.4 - - - +
74D THR* 1.3 64.8 + - - +
75D VAL* 3.6 25.4 - - + -
92D PHE* 3.6 26.2 - + - -
118D ILE* 3.6 26.2 - - + -
119D ALA 4.1 7.2 - - - -
120D PRO* 4.0 11.9 - - + -
136D LEU* 3.8 3.3 - - - +
137D ASN* 2.8 57.4 + - + +
139D GLU* 3.7 24.5 - - + -
162D VAL* 4.2 4.5 - - + -
163D ALA 3.0 15.3 - - - +
164D LEU* 4.0 12.1 - - + -
165D LEU* 4.2 2.7 - - - -
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Residues in contact with THR 74 (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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32C MET* 3.9 4.7 - - + -
33C ASN* 3.1 24.6 + - - -
73D PHE* 1.3 76.7 - - - +
75D VAL* 1.3 67.2 + - - +
124D THR* 4.6 2.2 - - - -
134D VAL* 3.8 21.1 - - + -
135D LYS 3.2 26.2 - - - +
136D LEU* 4.2 7.0 - - + -
137D ASN* 4.4 0.7 - - - +
161D CYS 3.8 0.3 - - - +
162D VAL* 3.3 6.1 - - - +
163D ALA* 2.9 44.8 + - - +
165D LEU* 4.2 12.6 - - + -
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Residues in contact with VAL 75 (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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33C ASN* 4.4 1.3 - - - -
73D PHE* 3.6 27.4 - - + -
74D THR* 1.3 81.4 - - - +
76D ARG* 1.3 71.9 + - - +
89D LYS 4.7 2.0 - - - +
90D GLU* 3.8 34.1 - - + +
92D PHE* 5.0 2.9 - - + -
120D PRO* 3.8 22.7 - - + -
122D GLU 5.0 0.4 + - - -
123D ILE* 3.7 4.7 - - + -
124D THR* 2.8 30.0 + - - -
135D LYS 4.8 0.8 + - - -
137D ASN* 4.5 4.8 - - - +
160D ALA* 4.9 2.5 - - + -
161D CYS 3.4 10.1 - - - +
162D VAL* 4.3 12.1 - - + -
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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