Contacts of the strand formed by residues 103 - 112 (chain K) in PDB entry 3IT8
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 LEU 103 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31H ARG* 5.3 0.2 - - - -
98K TYR* 4.1 12.6 - - + +
99K GLU* 3.6 2.6 - - - +
100K THR 3.0 28.9 + - - +
101K GLY 3.8 1.4 - - - +
102K LEU* 1.3 83.1 - - + +
104K PHE* 1.3 62.3 + - - +
213K ILE* 3.5 41.3 - - + -
215K LYS* 4.2 20.9 - - - +
228K TYR* 5.1 3.4 - - + +
284K PHE* 3.5 43.3 - - + -
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Residues in contact with PHE 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H ASN* 4.1 26.5 - - - -
31H ARG* 3.6 30.7 - - + -
32H ARG 5.1 4.9 - - - -
98K TYR* 3.2 25.5 + - - +
99K GLU* 4.1 14.6 - - + -
102K LEU 3.4 16.8 - - - -
103K LEU* 1.3 76.1 - - - +
105K GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K CYS* 3.2 5.4 - - - +
98K TYR* 2.9 50.5 + - - +
104K PHE* 1.3 78.9 - - - +
106K SER* 1.3 60.4 + - - -
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Residues in contact with SER 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K GLY 3.3 12.1 - - - -
97K CYS* 3.9 9.9 - - - +
98K TYR* 4.1 1.7 - - - -
105K GLY* 1.3 74.9 - - - -
107K TYR* 1.3 65.7 + - - +
159K GLU* 2.7 43.5 + - - +
163K CYS* 5.2 3.1 - - - -
164K SER* 5.8 3.4 - - - -
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Residues in contact with TYR 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K THR* 5.5 1.7 - - - +
3K LEU 3.5 17.3 + - - -
4K LYS* 3.6 17.3 - - - +
94K ILE* 3.8 12.6 - - + -
95K THR* 2.8 29.0 + - - -
96K GLY* 2.8 46.5 + - - +
97K CYS* 3.8 10.6 + - - -
98K TYR* 4.5 4.7 - + + -
106K SER* 1.3 80.0 - - - +
108K GLY* 1.3 60.6 + - - +
109K TYR* 4.1 6.5 - + + -
159K GLU* 3.5 14.3 - - - +
244K GLU* 6.0 0.2 - - - +
246K GLY 3.6 27.1 - - - -
247K GLU* 4.0 28.0 - - + +
248K PRO* 3.3 23.1 - - + +
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Residues in contact with GLY 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K ILE 3.2 8.7 - - - -
95K THR* 3.8 9.0 - - - -
107K TYR* 1.3 78.3 - - - +
109K TYR* 1.3 59.7 + - - +
119K ARG* 3.9 2.8 - - - +
120K TYR* 2.8 35.6 + - - +
155K LEU* 4.1 9.6 - - - -
159K GLU* 3.4 14.5 + - - +
247K GLU* 5.4 0.2 + - - -
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Residues in contact with TYR 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K SER 3.9 0.2 - - - +
93K LEU* 3.6 4.6 - - - +
94K ILE* 2.8 62.5 + - + +
107K TYR* 4.1 9.0 - + - -
108K GLY* 1.3 78.1 - - - +
110K VAL* 1.3 70.0 + - - +
111K GLU* 3.3 23.5 + - - -
118K ALA 3.3 12.8 - - - +
119K ARG* 3.8 9.4 - - + -
120K TYR 4.5 0.2 - - - +
127K PHE* 4.9 1.3 - - - -
130K MET* 3.6 23.1 - - + -
243K TYR* 3.7 14.8 - + - -
247K GLU* 3.7 35.9 - - + -
248K PRO* 3.5 10.3 - - + +
249K GLY* 3.2 24.4 + - - -
325K NAG 4.8 2.1 - - - +
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Residues in contact with VAL 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K LEU* 3.6 32.3 - - + -
92K SER 3.2 7.6 - - - +
93K LEU* 3.9 19.7 - - + -
109K TYR* 1.3 75.4 - - - +
111K GLU* 1.3 62.3 + - - +
117K LEU* 2.9 37.5 + - + +
118K ALA 2.7 17.0 + - - +
127K PHE* 4.0 17.3 - - + -
130K MET* 3.2 2.6 - - - +
140K MET* 4.0 20.6 - - + -
141K LEU* 4.2 13.9 - - + -
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Residues in contact with GLU 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91K LEU* 3.5 7.2 - - - +
92K SER* 2.9 46.9 + - - -
94K ILE* 4.0 12.6 - - + +
109K TYR* 3.3 22.8 + - + -
110K VAL* 1.3 75.4 - - - +
112K THR* 1.3 64.9 + - - +
115K GLY 3.9 4.9 - - - +
116K PRO* 3.9 17.3 - - + -
117K LEU* 3.9 1.6 - - - +
243K TYR* 3.1 20.1 + - - -
249K GLY* 5.4 1.4 - - - -
325K NAG 3.9 25.8 + - - +
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Residues in contact with THR 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K LEU* 6.1 0.2 - - - +
80K ILE* 4.7 5.0 - - - +
86K THR* 6.0 1.6 - - + +
88K THR* 3.3 14.6 + - + +
90K SER 3.8 7.4 + - - -
91K LEU* 3.6 17.8 - - - +
111K GLU* 1.3 77.9 - - - +
113K ALA* 1.3 63.6 + - - +
114K ASN* 2.8 41.5 - - + +
115K GLY* 2.8 30.8 + - - +
117K LEU* 4.1 17.2 - - + +
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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