Contacts of the strand formed by residues 74 - 80 (chain T) in PDB entry 3SDI
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 ILE 74 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69T VAL* 3.3 6.9 - - - +
70T VAL* 2.8 53.9 + - + +
72T ARG 3.7 1.0 - - - -
73T HIS* 1.3 105.1 - - + +
75T GLY* 1.3 73.6 + - - +
76T CYS* 4.2 1.8 - - - -
107T ILE* 3.9 10.8 - - + +
109T ILE* 3.7 21.5 - - + -
112T PHE* 3.8 48.7 - - + -
138T PHE* 4.8 0.2 - - + -
139T GLY* 3.4 10.5 - - - +
221T HIS* 4.3 4.2 - - - +
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Residues in contact with GLY 75 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T PHE* 3.8 12.6 - - - -
68T GLN 3.6 3.1 - - - -
73T HIS 4.2 0.2 + - - -
74T ILE* 1.3 74.7 - - - +
76T CYS* 1.3 62.1 + - - -
138T PHE* 2.9 29.9 - - - +
139T GLY 2.9 13.6 + - - -
215T CYS* 5.7 0.2 - - - +
221T HIS* 3.5 28.8 - - - -
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Residues in contact with CYS 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T PHE* 5.5 0.4 - - - -
66T LYS 4.2 1.2 - - - +
67T ILE* 3.5 6.7 - - - +
68T GLN* 2.8 43.0 + - - +
70T VAL* 3.7 26.9 - - - -
74T ILE* 4.2 5.4 - - - -
75T GLY* 1.3 78.6 - - - -
77T VAL* 1.3 60.5 + - - +
78T TYR* 4.7 2.3 - - + -
89T VAL* 3.8 25.1 - - + -
112T PHE* 4.3 9.0 - - - -
116T LEU* 5.3 2.2 - - - -
136T THR* 4.6 9.6 - - + -
137T ILE 3.5 4.3 - - - -
138T PHE* 3.7 14.8 - - + -
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Residues in contact with VAL 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37T SER* 4.0 16.2 - - - -
38T ILE 4.1 13.0 - - - +
48T PHE* 4.3 11.2 - - + -
49T ALA 4.5 1.3 - - - +
50T VAL* 3.7 33.2 - - + -
66T LYS* 4.8 3.1 - - + +
67T ILE* 3.8 26.2 - - + +
76T CYS* 1.3 74.9 - - - +
78T TYR* 1.3 67.1 + - - +
136T THR* 3.4 4.3 - - - +
137T ILE* 2.6 60.0 + - + +
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Residues in contact with TYR 78 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35T THR* 5.1 1.2 - - - +
37T SER* 3.8 9.3 + - - -
50T VAL* 4.7 6.4 - - - +
66T LYS* 4.0 24.3 + - + -
68T GLN* 2.8 31.7 + - - -
76T CYS 4.7 3.1 - - - -
77T VAL* 1.3 87.1 - - - +
79T SER* 1.3 65.7 + - - +
82T ILE* 3.8 38.5 - - + +
85T GLY* 3.6 35.0 - - - -
86T ARG* 3.4 17.3 - - - +
89T VAL* 3.9 8.7 - - + -
134T VAL* 4.3 11.2 - - + -
135T SER 3.3 14.1 - - - +
136T THR* 3.9 20.0 - - + +
137T ILE 4.7 0.2 - - - +
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Residues in contact with SER 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31T VAL* 3.6 10.7 - - - +
34T GLY* 5.2 0.2 - - - -
35T THR* 2.7 30.6 + - - +
37T SER* 2.9 19.4 + - - -
78T TYR* 1.3 73.5 + - - +
80T GLY* 1.3 60.0 + - - +
82T ILE* 5.4 1.1 - - - -
134T VAL* 3.3 5.3 - - - -
135T SER 3.0 29.2 + - - -
165T THR* 3.0 20.0 + - - +
166T GLY* 4.0 11.4 - - - -
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Residues in contact with GLY 80 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30T ALA 3.8 18.8 - - - -
31T VAL* 4.0 4.5 - - - -
34T GLY* 4.3 12.0 - - - -
35T THR 5.2 0.2 - - - +
79T SER* 1.3 76.8 - - - +
81T LEU* 1.3 67.0 + - - +
82T ILE* 3.4 14.8 + - - +
133T GLY 3.2 9.6 - - - -
134T VAL* 3.9 0.2 - - - -
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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