Contacts of the strand formed by residues 64 - 68 (chain A) in PDB entry 4PH8
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 TRP 64 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE 4.3 5.6 - - - -
37A SER* 4.7 0.7 - - - -
38A ALA* 4.2 7.4 - - + -
55A LEU* 3.9 15.5 - - + -
56A TRP* 4.3 4.0 - - - +
57A GLY* 3.8 19.1 - - - +
62A ASN 3.7 9.1 + - - -
63A LYS* 1.3 76.8 - - - +
65A VAL* 1.3 60.4 + - - +
66A LEU 4.1 0.4 - - - -
76A TYR 3.5 1.6 - - - +
77A THR* 3.5 1.4 - - - -
78A LEU* 2.7 41.8 + - + +
80A PRO* 3.6 24.8 - - + +
95A ALA 5.3 0.4 + - - -
97A ILE* 4.2 6.1 - - + +
110A ALA* 3.7 39.7 - - + -
111A SER* 4.1 3.4 - - - -
112A VAL* 3.3 44.6 - - + -
128A MET* 3.8 17.5 - - + -
129A ILE 5.5 0.2 - - - -
130A LEU* 3.4 37.2 - - + +
151A ILE* 5.1 0.4 - - + -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.9 15.6 + - - +
59A GLY* 3.4 37.0 - - - +
60A PRO* 4.9 0.4 - - + -
63A LYS 3.7 0.8 + - - -
64A TRP* 1.3 74.5 - - - +
66A LEU* 1.3 62.1 + - - +
67A GLN* 3.5 12.9 + - + +
75A LYS* 3.9 37.5 - - + +
76A TYR 3.4 5.8 - - - +
77A THR* 4.3 11.7 - - - +
127A THR 3.4 2.8 - - - +
128A MET* 3.3 27.2 - - - +
129A ILE 4.2 3.6 + - - -
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Residues in contact with LEU 66 (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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36A PHE* 4.2 18.4 - - + -
64A TRP 4.1 1.0 + - - -
65A VAL* 1.3 69.7 - - - +
67A GLN* 1.3 58.2 + - - +
75A LYS* 3.1 5.2 - - - -
76A TYR* 2.9 46.6 + - + +
78A LEU* 4.4 5.8 - - + -
114A VAL* 3.8 26.9 - - + -
126A TYR* 3.7 35.7 - - + -
127A THR* 3.6 4.9 - - - +
128A MET* 3.9 28.4 - - + +
151A ILE* 5.0 2.5 - - + +
153A LEU* 4.0 27.1 - - + +
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.2 13.2 - - + +
66A LEU* 1.3 72.5 - - - +
68A HIS* 1.3 79.5 + - - +
69A ALA* 3.5 1.4 + - - -
71A VAL 3.6 0.2 + - - -
72A ALA* 2.9 31.4 + - - +
74A GLN 3.3 17.5 + - - -
75A LYS* 3.4 28.3 + - - +
126A TYR* 3.3 4.4 - - - -
127A THR* 2.8 45.4 + - - +
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Residues in contact with HIS 68 (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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67A GLN* 1.3 87.9 + - - +
69A ALA* 1.3 67.5 + - + +
70A LYS* 3.3 43.9 + - + -
71A VAL* 3.5 22.7 + - + +
72A ALA* 5.2 0.3 - - - -
74A GLN* 3.0 40.1 + - + +
122A ILE* 4.7 5.3 - - + +
123A PRO 3.1 23.5 + - - -
124A GLY* 3.8 9.0 - - - -
125A GLU 3.6 9.2 - - - -
126A TYR* 3.5 37.1 - + + -
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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