Contacts of the strand formed by residues 94 - 99 (chain A) in PDB entry 2IVF
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 PHE 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TRP* 3.5 13.6 - - - -
80A GLY 2.7 41.4 + - - +
82A HIS* 3.6 14.8 - + - -
92A CYS* 3.5 23.6 - - + -
93A LYS* 1.3 75.6 - - - +
95A TYR* 1.3 65.0 + - - +
96A VAL* 4.6 2.0 - - + -
106A GLU* 3.7 12.3 - - + -
107A GLU* 3.3 29.6 - - - -
108A GLN* 3.7 23.3 - - + -
109A ALA 4.6 1.1 - - - -
126A GLY* 3.9 2.7 - - - -
130A GLY 4.2 0.2 - - - -
131A SER* 3.4 36.6 - - - -
656A TYR* 4.8 1.3 - - - +
1984A SF4 3.5 32.5 - - - -
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Residues in contact with TYR 95 (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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77A VAL* 3.5 23.8 - - + -
78A ASN 3.6 2.5 - - - -
79A TRP* 3.4 31.1 - + - -
94A PHE* 1.3 72.4 - - - +
96A VAL* 1.3 60.9 + - - +
97A TYR* 3.7 16.3 - - + -
106A GLU* 3.1 8.3 - - - +
107A GLU 2.7 43.5 + - - +
108A GLN 4.1 0.4 - - - -
109A ALA* 3.6 22.6 + - + +
111A GLN* 3.6 23.6 + - - -
347B ASP* 4.2 7.1 + - - -
348B PRO* 3.9 34.3 - - + -
349B LEU* 3.6 30.9 - - + +
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Residues in contact with VAL 96 (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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76A LYS 3.7 0.5 - - - +
77A VAL* 3.1 6.4 - - - -
78A ASN 2.8 35.1 + - - +
79A TRP 4.1 0.9 - - - -
80A GLY* 3.5 33.9 - - - +
94A PHE* 4.2 2.2 - - + +
95A TYR* 1.3 74.7 - - - +
97A TYR* 1.3 61.8 + - - +
98A VAL* 3.7 5.5 + - + +
103A VAL* 3.8 18.4 - - + -
105A ARG 3.9 2.7 - - - -
106A GLU* 4.5 0.7 - - + +
656A TYR* 3.7 40.4 - - + +
677A SER* 3.5 27.1 - - - +
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Residues in contact with TYR 97 (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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72A TRP* 4.6 0.7 - + - -
74A TRP* 3.6 41.3 - + + -
76A LYS 3.5 3.4 - - - -
77A VAL* 3.7 13.2 - - + -
95A TYR* 3.7 30.9 - - + -
96A VAL* 1.3 72.7 - - - +
98A VAL* 1.3 61.0 + - - +
103A VAL* 3.7 3.0 - - - -
104A TRP* 2.8 44.7 + + + +
105A ARG* 2.8 56.0 + - + +
107A GLU* 3.8 7.5 + - + +
348B PRO* 2.5 47.7 + - - +
349B LEU* 4.6 0.7 - - + -
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Residues in contact with VAL 98 (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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74A TRP* 3.9 0.9 - - - +
75A ASP* 2.9 26.4 + - + +
76A LYS* 2.9 50.1 + - + -
78A ASN* 4.2 3.8 - - - +
96A VAL* 4.3 7.9 - - + +
97A TYR* 1.3 76.1 - - - +
99A ARG* 1.3 66.6 + - - +
101A GLY* 4.1 10.3 - - - +
102A ILE 3.2 24.2 - - - +
103A VAL* 4.7 1.3 - - + -
677A SER* 4.1 14.8 - - - -
678A VAL* 4.0 19.5 - - + -
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Residues in contact with ARG 99 (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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70A LYS 4.7 2.4 + - - -
71A GLU* 2.8 50.9 + - - +
73A LYS* 2.9 32.2 + - - +
74A TRP* 3.9 3.4 - - - +
75A ASP* 3.5 20.2 - - - +
97A TYR 4.1 0.4 + - - -
98A VAL* 1.3 77.2 - - - +
100A ASN* 1.3 87.8 + - - +
101A GLY 3.0 1.3 - - - -
102A ILE* 2.9 23.1 + - - +
104A TRP* 3.4 44.4 - - + +
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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