Contacts of the strand formed by residues 60 - 64 (chain H) in PDB entry 3H2V
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 60 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58H MET* 3.6 26.0 - - + +
59H ARG* 1.3 91.2 - - - +
61H ILE* 1.3 61.3 + - - +
86H TYR* 6.3 0.4 - - - -
98H VAL 3.5 4.9 - - - +
99H THR* 2.8 34.7 + - - +
127H LEU* 3.7 9.0 - - - +
128H GLN* 2.8 54.9 + - + +
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Residues in contact with ILE 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59H ARG 4.0 0.6 + - - -
60H LYS* 1.3 74.1 - - - +
62H LEU* 1.3 57.1 + - - +
63H ILE* 4.1 20.4 - - + -
79H LEU* 5.0 7.4 - - + -
98H VAL* 3.0 36.9 + - + +
100H LEU* 4.8 9.9 - - + -
106H ALA* 3.8 27.6 - - + +
109H ALA* 4.5 14.6 - - + -
110H ILE* 3.8 31.0 - - + -
125H VAL* 3.8 22.4 - - + -
126H GLN 3.5 6.7 - - - +
127H LEU* 4.2 0.9 - - + -
128H GLN* 2.4 25.1 - - - +
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Residues in contact with LEU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012C SER* 6.1 0.4 - - - -
1013C ASP* 5.3 3.1 - - - +
61H ILE* 1.3 75.1 - - - +
63H ILE* 1.3 63.5 + - - +
64H ARG* 4.4 28.3 - - + +
95H THR* 4.0 22.2 - - + -
96H ALA 3.5 17.3 - - - +
97H PHE* 3.9 24.0 - - + -
124H SER 3.5 4.3 - - - +
126H GLN* 2.8 42.2 + - - +
128H GLN* 3.8 14.8 - - + +
129H PRO* 3.3 32.8 - - + -
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ILE* 4.1 10.8 - - + -
62H LEU* 1.3 74.3 - - - +
64H ARG* 1.3 67.2 + - - +
66H LEU* 3.6 32.1 - - + -
75H VAL* 4.6 3.1 - - + -
78H LEU* 4.3 8.7 - - + -
79H LEU* 4.3 20.2 - - + -
95H THR* 3.0 9.5 - - - -
96H ALA* 2.9 42.4 + - + +
98H VAL* 4.0 26.2 - - + -
123H LEU* 4.4 12.6 - - + -
124H SER 3.5 4.3 - - - +
125H VAL* 3.9 24.7 - - + -
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Residues in contact with ARG 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009C THR* 3.2 29.0 + - - +
1010C ASN 4.7 1.0 + - - -
1011C ILE 3.0 29.5 + - - -
1012C SER* 4.3 1.6 - - - +
1013C ASP* 3.4 33.5 + - - +
62H LEU* 4.4 24.0 - - + +
63H ILE* 1.3 77.0 - - - +
65H GLY* 1.3 63.2 + - - +
66H LEU 3.4 2.4 + - - -
94H GLY 3.9 3.4 - - - -
95H THR* 4.2 15.7 - - + -
123H LEU* 3.5 7.1 - - - +
124H SER* 3.0 48.2 + - - +
126H GLN* 4.0 11.9 - - - +
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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