Contacts of the strand formed by residues 99 - 108 (chain C) in PDB entry 4DCK
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 TYR 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1895A THR* 4.7 0.6 - - - +
1898A ARG* 3.1 23.6 - - - -
21C TYR* 6.3 1.8 - + - -
23C ARG* 3.5 55.0 + - + +
94C VAL* 2.8 35.7 - - - +
95C PHE* 2.8 18.3 + + - +
96C GLU* 5.6 3.8 - - - -
97C ASN 3.8 0.2 - - - -
98C TYR* 1.3 108.9 - + + +
100C VAL* 1.3 58.6 + - - +
101C THR* 5.0 0.2 - - - -
140C HIS* 3.6 44.0 - + + -
141C PHE 3.8 12.1 - - - +
142C LEU* 5.3 0.9 - - + -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892A ILE* 3.9 38.4 - - + -
1893A THR 5.6 1.3 - - - -
1894A THR* 5.8 0.2 - - - -
1895A THR* 5.4 4.3 - - + -
92C GLU* 4.7 0.2 - - + -
93C SER 3.3 8.1 - - - +
94C VAL* 4.5 4.3 - - + -
99C TYR* 1.3 77.1 - - - +
101C THR* 1.3 65.6 + - - +
102C TYR* 3.3 37.1 - - + +
139C ALA 3.5 2.6 - - - +
141C PHE* 2.9 40.7 + - - +
142C LEU* 4.9 5.2 - - + -
143C PRO* 3.8 21.8 - - + -
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LYS 3.3 4.2 - - - +
92C GLU* 3.4 3.3 - - - -
93C SER* 2.5 50.6 + - - +
95C PHE* 4.4 8.5 - - + -
100C VAL* 1.3 77.2 - - - +
102C TYR* 1.3 64.8 + - - +
117C TYR* 3.6 19.0 - - - -
134C LYS* 3.5 35.8 - - + +
139C ALA* 3.4 22.9 - - + +
140C HIS* 4.1 16.8 - - + -
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Residues in contact with TYR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1892A ILE 4.8 0.9 + - - -
20C LEU* 3.7 27.7 - - + +
51C LEU* 3.9 11.1 - - + +
59C VAL* 4.0 28.5 - - + -
61C ILE* 4.3 11.2 - - + -
90C PHE* 4.1 18.6 - - + -
91C LYS 3.2 5.2 - - - -
92C GLU* 4.1 14.5 + - + -
100C VAL* 3.3 30.7 - - + +
101C THR* 1.3 76.9 - - - +
103C SER* 1.3 60.4 + - - +
117C TYR* 3.4 6.4 - - - -
118C LEU* 2.9 53.2 + - + +
139C ALA 4.9 1.4 + - - -
141C PHE* 4.0 28.2 - + + -
143C PRO* 3.7 12.6 - - - +
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Residues in contact with SER 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.2 10.4 - - - -
91C LYS* 2.7 53.3 + - - +
93C SER* 6.2 0.3 - - - -
102C TYR* 1.3 74.3 - - - +
104C SER* 1.3 66.9 + - - +
115C GLY* 5.0 2.2 - - - -
116C TRP 3.1 18.2 - - - -
117C TYR* 3.5 31.0 + - - +
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Residues in contact with SER 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C MET* 4.0 28.4 + - - +
89C LYS 4.3 4.5 - - - -
90C PHE* 4.5 5.4 - - - -
91C LYS* 4.9 2.1 - - - +
103C SER* 1.3 79.4 + - - +
105C MET* 1.3 62.6 + - - +
106C ILE* 3.2 4.2 + - - +
107C TYR* 2.8 56.4 + - - +
108C ARG* 4.5 8.8 + - - -
115C GLY* 5.9 0.9 - - - -
116C TRP* 2.9 11.3 + - - +
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Residues in contact with MET 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1873A ILE* 5.7 5.6 - - + -
1877A GLU* 4.2 21.1 - - + +
58C VAL* 4.0 20.0 - - + -
86C PRO 5.0 3.1 + - - +
89C LYS* 3.4 44.8 + - + +
91C LYS* 3.6 44.2 - - - +
103C SER 3.5 0.6 + - - -
104C SER* 1.3 74.2 + - - +
106C ILE* 1.3 70.1 + - + +
108C ARG* 4.6 9.6 + - - +
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Residues in contact with ILE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C PRO* 3.5 43.1 - - + +
87C GLU* 4.0 8.1 - - + +
104C SER* 3.9 6.1 - - - +
105C MET* 1.3 91.5 - - + +
107C TYR* 1.3 96.7 + - + +
108C ARG* 4.3 3.8 + - - +
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Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C MET* 3.2 25.4 - - + -
73C ASN 3.3 20.4 - - - -
74C SER* 3.4 33.1 - - - -
87C GLU* 2.6 25.0 + - + +
104C SER* 2.8 36.7 + - - +
106C ILE* 1.3 102.6 - - + +
108C ARG* 1.3 69.2 + - - +
116C TRP* 3.5 30.4 + + + -
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1873A ILE* 5.0 19.2 - - - +
104C SER 4.5 12.9 + - - -
105C MET* 4.6 10.3 + - - +
106C ILE 4.3 3.8 + - - +
107C TYR* 1.3 81.0 + - - +
109C GLN* 1.3 62.6 + - - +
110C GLN* 2.5 35.1 + - - +
113C GLY* 3.6 32.9 + - - -
114C ARG 3.2 15.3 - - - +
115C GLY* 4.0 15.2 - - - +
116C TRP* 3.5 14.1 - - - +
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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