Contacts of the strand formed by residues 99 - 106 (chain A) in PDB entry 1D8V
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 ARG 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ASP* 3.0 15.8 + - + +
79A VAL* 3.8 26.5 - - + +
80A SER* 3.3 13.4 + - - -
95A PHE* 4.4 0.3 - - - -
98A THR* 1.3 95.2 - - - +
100A LYS* 1.3 73.4 + - - +
101A ILE* 4.3 6.1 - - + -
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Residues in contact with LYS 100 (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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80A SER 3.4 5.4 - - - -
82A PHE* 3.7 6.3 - - + -
91A TYR* 3.7 19.4 + - + +
95A PHE* 3.6 26.7 - - + -
98A THR 4.1 4.7 - - - +
99A ARG* 1.3 95.2 - - - +
101A ILE* 1.3 69.6 + - - +
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Residues in contact with ILE 101 (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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79A VAL* 3.3 35.0 - - + -
80A SER 3.1 7.3 + - - -
81A TYR* 2.6 43.4 - - + +
82A PHE* 3.2 2.6 + - - -
91A TYR* 5.1 0.4 - - - -
99A ARG* 4.3 8.1 - - + -
100A LYS* 1.3 88.6 - - - +
102A THR* 1.3 68.0 + - - +
103A LEU* 4.9 3.6 - - + +
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Residues in contact with THR 102 (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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82A PHE* 2.6 25.8 - - + +
83A PHE 2.4 36.8 - - - +
84A LYS* 4.0 7.0 - - + +
88A PRO* 5.4 3.8 - - + -
91A TYR* 2.7 31.7 + - + -
101A ILE* 1.3 78.5 - - - +
103A LEU* 1.3 67.4 + - - +
104A PRO* 3.6 3.5 - - - +
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Residues in contact with LEU 103 (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 TYR* 5.6 1.3 - - + +
81A TYR* 4.3 17.5 - - + -
82A PHE* 3.0 31.2 + - - +
83A PHE* 4.1 19.4 - - + -
84A LYS* 4.5 2.3 + - - +
101A ILE* 4.9 4.0 - - + +
102A THR* 1.3 81.6 - - - +
104A PRO* 1.3 66.3 - - + +
105A TYR* 2.6 47.3 + - + +
140A TYR* 3.0 39.0 - - + +
145A ALA* 5.6 1.1 - - + -
146A PRO* 6.2 1.1 - - + -
149A LEU* 6.0 3.1 - - + -
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Residues in contact with PRO 104 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 5.1 10.4 - - + +
102A THR 3.6 3.8 - - - +
103A LEU* 1.3 86.7 - - + +
105A TYR* 1.3 74.9 + - + +
106A THR* 3.9 6.1 + - - +
111A ASN* 5.2 1.7 + - - -
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Residues in contact with TYR 105 (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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83A PHE* 3.3 23.4 - + + +
84A LYS* 3.0 17.7 + - - +
103A LEU* 2.6 36.7 + - + +
104A PRO* 1.3 88.9 - - + +
106A THR* 1.3 61.1 + - - +
111A ASN* 3.9 22.7 - - + +
112A LEU* 3.8 14.1 - - + -
114A THR* 6.2 0.7 - - + -
115A ALA* 3.2 34.8 - - + +
140A TYR* 5.6 1.8 - - - -
142A ALA 5.9 1.8 - - - -
146A PRO* 5.3 9.4 - - + -
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Residues in contact with THR 106 (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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83A PHE* 3.3 3.0 - - - -
84A LYS* 3.7 16.4 - - + +
85A GLU* 3.4 29.2 - - + +
104A PRO 4.6 4.5 - - - +
105A TYR* 1.3 78.1 - - - +
107A GLY* 1.3 52.9 + - - +
108A ASN* 2.3 42.0 + - - +
111A ASN* 2.3 45.5 + - - +
112A LEU* 3.7 9.5 - - - +
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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