Contacts of the strand formed by residues 74 - 79 (chain B) in PDB entry 3H44
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 LYS 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ARG* 6.3 0.2 - - - +
67B LEU 3.9 3.6 - - - -
68B GLU* 4.6 12.8 - - + +
72B GLY 4.0 11.4 - - - +
73B ILE* 1.3 77.2 - - - +
75B VAL* 1.3 53.5 + - - +
252B ASN 4.6 12.0 + - - +
254B MET 3.1 16.8 + - - +
255B ALA* 3.2 11.2 - - + -
256B VAL 2.7 31.0 + - - -
441B LEU* 4.1 23.3 - - + +
442B HIS* 4.4 24.4 + - - +
446B LEU* 4.3 21.8 - - + -
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Residues in contact with VAL 75 (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 GLY* 3.1 4.9 - - - -
67B LEU* 2.8 58.0 + - + +
69B LEU* 4.0 8.5 - - + -
73B ILE* 3.7 20.0 - - + +
74B LYS* 1.3 80.8 - - - +
76B LEU* 1.3 72.2 + - - +
77B LEU* 4.0 21.5 - - + -
256B VAL* 3.0 16.6 - - + +
258B VAL* 5.4 0.2 - - + -
271B VAL* 4.2 20.9 - - + -
441B LEU* 4.2 5.3 - - - +
446B LEU* 4.5 6.3 - - - +
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Residues in contact with LEU 76 (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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54B ILE* 4.3 13.5 - - + -
64B TYR* 3.9 27.8 - - + -
65B ARG 3.7 19.7 - - - +
66B GLY* 3.8 5.8 - - - +
75B VAL* 1.3 77.1 - - - +
77B LEU* 1.3 76.4 + - - +
78B ILE* 4.0 16.4 - - + -
256B VAL 2.8 7.1 + - - +
257B VAL* 3.3 16.9 - - + +
258B VAL 3.1 24.4 + - - +
437B ILE* 3.7 23.6 - - + -
441B LEU* 4.0 7.6 - - + +
446B LEU* 5.4 0.4 - - + +
449B VAL* 4.3 10.1 - - + -
450B LEU* 4.4 9.0 - - + -
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Residues in contact with LEU 77 (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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63B GLU 3.7 0.3 - - - +
64B TYR* 3.4 6.9 - - - -
65B ARG* 2.9 42.0 + - + +
67B LEU* 3.6 24.2 - - + -
75B VAL* 4.0 4.3 - - + -
76B LEU* 1.3 83.5 - - - +
78B ILE* 1.3 63.3 + - - +
79B SER 4.2 0.4 - - - -
258B VAL* 3.5 9.9 - - + -
264B LEU* 3.8 13.9 - - + +
267B LEU* 3.8 20.6 - - + +
268B THR* 3.4 33.4 - - - +
271B VAL* 3.6 30.7 - - + -
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Residues in contact with ILE 78 (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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62B ARG* 4.0 24.9 - - + -
63B GLU 3.4 2.7 - - - -
64B TYR* 3.5 29.4 - - + -
76B LEU* 4.0 9.0 - - + -
77B LEU* 1.3 76.0 - - - +
79B SER* 1.3 62.9 + - - +
80B ASP 3.8 0.2 + - - -
257B VAL* 3.7 26.9 - - + -
258B VAL 2.9 11.9 + - - +
259B LEU* 3.3 37.6 - - + -
260B GLY 3.2 25.1 + - - +
267B LEU* 3.3 7.1 - - - +
433B TYR* 4.1 17.7 - - + -
434B THR* 4.7 1.8 - - + -
437B ILE* 5.1 1.8 - - + -
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Residues in contact with SER 79 (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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61B LYS 4.9 0.2 - - - +
62B ARG* 3.6 2.6 - - - -
63B GLU* 2.8 49.8 + - - +
77B LEU 4.2 0.6 - - - -
78B ILE* 1.3 73.8 - - - +
80B ASP* 1.3 58.7 + - - +
81B PRO* 3.5 14.9 - - - +
260B GLY 3.6 2.9 - - - -
261B ARG 3.5 8.5 + - - -
262B GLU 3.0 23.1 + - - -
263B SER* 4.0 4.7 - - - -
264B LEU* 4.2 17.2 - - - +
267B LEU* 4.1 2.7 - - - +
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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