Contacts of the strand formed by residues 49 - 56 (chain B) in PDB entry 3N2Z
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 SER 49 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B TYR* 1.3 75.4 + - - +
50B VAL* 1.3 64.4 + - - +
51B LEU* 3.6 21.1 + - - +
73B LEU* 3.3 6.9 - - - -
74B VAL* 2.9 36.7 + - - -
76B ASP* 5.3 4.5 + - - -
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Residues in contact with VAL 50 (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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48B TYR* 3.7 27.6 + - + +
49B SER* 1.3 70.9 - - - +
51B LEU* 1.3 67.2 + - - +
52B TYR* 4.0 20.3 - - + +
71B ARG* 3.7 34.8 - - + +
72B TYR 3.9 2.2 - - - -
73B LEU* 3.9 8.3 - - + -
97B ILE* 5.5 7.0 - - + -
127B GLU* 5.4 0.2 - - - +
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Residues in contact with LEU 51 (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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49B SER* 4.2 15.0 - - - +
50B VAL* 1.3 79.5 - - - +
52B TYR* 1.3 66.9 + - - +
71B ARG* 3.4 6.8 - - - +
72B TYR* 2.8 64.8 + - + +
74B VAL* 3.6 35.2 - - + -
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Residues in contact with TYR 52 (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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50B VAL* 4.0 20.4 - - + +
51B LEU* 1.3 80.9 - - - +
53B PHE* 1.3 62.7 + - - +
69B ASN* 4.0 27.8 - - + +
70B GLN 3.4 5.4 - - - -
71B ARG* 3.7 34.9 - - + -
72B TYR* 3.7 7.0 + - - -
127B GLU* 2.7 40.2 + - + -
160B HIS* 5.3 1.9 + - - -
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Residues in contact with PHE 53 (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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52B TYR* 1.3 74.4 - - - +
54B GLN* 1.3 76.5 + - + +
55B GLN* 3.4 45.4 + - + +
69B ASN* 4.2 3.4 - - - -
70B GLN* 2.9 32.1 + - - +
72B TYR* 3.6 19.1 - - + -
156B GLU* 3.9 28.9 - - + -
157B LEU* 3.8 15.0 - - + -
160B HIS* 3.5 39.5 - + + -
163B ARG* 4.5 8.5 - - - -
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Residues in contact with GLN 54 (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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53B PHE* 1.3 95.5 - - + +
55B GLN* 1.3 60.3 + - - +
67B THR* 3.1 37.1 + - + +
68B PHE* 3.5 7.2 + - - +
69B ASN* 3.9 22.4 + - - +
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Residues in contact with GLN 55 (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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53B PHE* 3.4 35.8 - - + +
54B GLN* 1.3 72.5 - - - +
56B LYS* 1.3 65.1 + - - +
59B HIS* 3.5 22.2 - - - -
67B THR* 3.2 7.9 - - - -
68B PHE* 2.8 53.9 + - + +
70B GLN* 2.9 33.6 + - + +
153B ASP* 2.9 34.5 + - - +
156B GLU* 3.5 10.4 - - - +
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Residues in contact with LYS 56 (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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55B GLN* 1.3 78.4 + - - +
57B VAL* 1.3 64.4 + - - +
58B ASP 4.0 17.0 - - - +
59B HIS* 3.6 22.4 + - + +
64B THR 6.1 0.9 - - - +
65B VAL* 5.6 8.1 - - + +
66B LYS 3.9 6.1 - - - +
67B THR* 4.3 11.7 - - + -
68B PHE* 3.8 1.4 - - - -
123B ARG* 3.2 15.2 + - - -
156B GLU* 5.1 10.1 + - - +
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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