Contacts of the strand formed by residues 137 - 143 (chain B) 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 ASN 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU 3.5 0.9 - - - +
72B LYS* 3.1 8.7 - - - +
73B PHE* 2.7 63.4 + - + +
74B THR* 4.3 4.9 - - - +
75B VAL 4.5 0.4 - - - +
120B PRO* 3.3 19.0 - - + +
121B ASP* 2.9 13.0 + - - +
122B GLU* 2.9 49.2 + - - +
135B LYS 3.6 7.0 + - - -
136B LEU* 1.3 76.1 - - - +
138B VAL* 1.3 63.3 + - - +
139B GLU* 5.3 1.6 - - + +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 4.0 28.5 - - + +
71B LEU 3.2 7.6 - - - +
72B LYS* 4.1 22.2 - - + +
121B ASP* 5.2 3.1 - - - +
136B LEU* 4.1 7.8 + - + +
137B ASN* 1.3 77.9 - - - +
139B GLU* 1.3 78.4 + - - +
140B GLU* 5.2 1.3 - - + +
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE 3.7 1.7 - - - +
70B GLU* 3.7 0.8 - - - -
71B LEU* 2.8 36.6 + - + +
73B PHE* 3.7 31.0 - - + -
118B ILE* 4.1 13.7 - - + -
119B ALA 3.5 17.4 - - - +
121B ASP* 4.1 21.0 + - - +
137B ASN* 4.2 1.3 - - + +
138B VAL* 1.3 83.9 - - - +
140B GLU* 1.3 60.5 + - - +
141B ARG* 2.9 32.1 + - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 4.0 16.7 - - + -
69B ILE 3.2 19.5 - - - +
70B GLU* 3.9 15.8 - - + +
138B VAL* 5.2 1.7 - - + +
139B GLU* 1.3 74.5 + - - +
141B ARG* 1.3 88.2 + - - +
170B TYR* 2.6 41.0 + - - -
172B LYS* 5.7 0.3 + - - -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.6 0.9 - - - -
69B ILE* 2.7 38.7 + - + +
71B LEU* 6.1 0.7 - - + -
94B LEU* 4.1 15.5 - - + -
115B ILE* 4.1 19.1 - - + -
116B ASP* 2.5 36.0 + - + +
117B THR 3.6 12.5 + - - -
118B ILE* 3.9 25.2 - - + +
119B ALA 5.0 1.8 - - - +
139B GLU* 2.9 39.1 + - - +
140B GLU* 1.3 94.2 + - - +
142B SER* 1.3 59.0 + - - +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ARG* 2.9 41.5 + - - -
67B ILE 3.2 13.9 - - - -
68B PHE* 3.8 22.3 - - - -
69B ILE* 5.3 0.2 - - - -
115B ILE* 4.5 7.6 - - - +
141B ARG* 1.3 77.0 - - - +
143B VAL* 1.3 69.1 + - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU 3.9 0.5 - - - +
66B ARG* 3.3 9.6 - - - +
67B ILE* 2.9 41.3 + - + +
69B ILE* 3.8 16.2 - - + -
96B TYR* 3.4 45.3 - - + +
115B ILE* 3.3 34.3 - - + -
142B SER* 1.3 79.9 - - - +
144B GLY* 1.3 63.4 + - - +
146B LEU* 4.4 7.1 - - + +
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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