Contacts of the strand formed by residues 134 - 142 (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 VAL 134 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31T VAL* 3.7 5.8 - - - +
78T TYR* 4.3 11.7 - - + -
79T SER 3.3 13.2 - - - +
80T GLY* 3.9 1.1 - - - -
81T LEU 3.1 34.5 - - - +
84T ASP* 4.0 9.4 - - + +
85T GLY* 3.6 27.6 - - - +
88T LEU* 4.7 7.4 - - + -
132T PHE* 3.2 13.9 + - + +
133T GLY* 1.3 83.8 - - - +
135T SER* 1.3 60.0 + - - +
136T THR* 4.0 13.0 + - - +
151T LEU 4.3 1.0 - - - +
152T GLU 4.3 0.3 - - - -
153T PRO* 3.2 23.4 - - - +
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Residues in contact with SER 135 (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* 3.4 15.9 - - - +
78T TYR* 3.3 2.4 - - - -
79T SER 3.0 28.5 + - - -
134T VAL* 1.3 74.4 - - - +
136T THR* 1.3 60.7 + - - +
150T MET* 4.2 4.0 - - - +
151T LEU 3.2 12.1 + - - -
152T GLU* 2.7 31.0 + - - -
153T PRO* 4.4 1.1 - - - -
165T THR* 3.3 31.0 + - - +
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Residues in contact with THR 136 (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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76T CYS* 4.6 9.9 - - + -
77T VAL 3.4 14.8 - - - +
78T TYR* 3.9 19.2 - - + +
88T LEU* 3.6 28.7 - - + +
89T VAL* 5.7 2.5 - - + -
116T LEU* 5.2 2.5 - - + -
134T VAL* 4.0 7.3 - - - +
135T SER* 1.3 75.2 + - - +
137T ILE* 1.3 67.3 + - - +
138T PHE* 4.0 20.4 - - + -
149T TYR 3.9 0.3 - - - +
150T MET* 3.2 4.6 - - - +
151T LEU* 2.8 39.2 + - - +
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Residues in contact with ILE 137 (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* 3.2 46.0 - - - +
38T ILE* 3.9 5.8 - - - +
39T GLY* 3.9 27.1 - - - +
48T PHE* 4.0 5.9 - - + -
76T CYS* 3.5 0.3 - - - -
77T VAL* 2.6 46.4 + - + +
136T THR* 1.3 76.9 - - - +
138T PHE* 1.3 65.6 + - - +
148T LEU* 4.0 10.5 - - + -
149T TYR 3.3 10.5 - - - +
150T MET* 4.1 17.7 - - + -
163T ALA* 4.3 6.5 - - + +
164T ALA* 4.2 5.2 - - - -
165T THR* 3.7 17.5 - - + +
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Residues in contact with PHE 138 (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* 3.6 9.6 - - - -
74T ILE* 4.6 0.9 - - + -
75T GLY 2.9 18.8 - - - +
76T CYS* 3.7 14.4 - - + -
109T ILE* 4.8 2.2 - - + -
112T PHE* 3.9 23.1 - + - -
113T ALA* 3.8 34.3 - - + -
116T LEU* 3.9 18.2 - - + -
136T THR* 4.0 18.6 - - + -
137T ILE* 1.3 79.9 - - - +
139T GLY* 1.3 62.4 + - - +
148T LEU* 3.6 3.1 - - - +
149T TYR* 2.9 60.4 + + + +
151T LEU* 4.1 22.7 - - + -
157T TYR* 5.4 2.0 - - + -
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Residues in contact with GLY 139 (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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46T VAL* 3.9 0.9 - - - -
48T PHE* 3.2 16.4 - - - -
73T HIS 3.8 0.2 - - - +
74T ILE* 3.4 5.2 - - - +
75T GLY 2.9 30.9 + - - -
109T ILE* 3.9 18.8 - - - -
138T PHE* 1.3 78.9 - - - +
140T GLY* 1.3 56.6 + - - -
147T HIS 3.2 12.1 - - - -
215T CYS* 5.1 0.5 - - - +
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Residues in contact with GLY 140 (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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46T VAL* 3.7 14.6 - - - +
73T HIS 3.3 13.7 - - - -
109T ILE* 3.5 16.1 - - - +
139T GLY* 1.3 74.6 - - - -
141T VAL* 1.3 62.9 + - - -
145T GLY 3.9 0.2 - - - +
146T ALA* 3.4 1.3 - - - -
147T HIS 2.9 30.9 + - - -
215T CYS* 4.0 3.6 - - - -
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Residues in contact with VAL 141 (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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44T ASP 3.9 18.8 - - - +
45T GLY* 4.3 3.6 - - - -
73T HIS* 3.7 22.9 + - - +
109T ILE* 4.5 1.6 - - - -
140T GLY* 1.3 75.0 - - - +
142T ASP* 1.3 69.4 + - - +
145T GLY* 3.4 18.8 - - - +
146T ALA* 4.3 2.5 - - + +
215T CYS* 3.6 39.6 - - - +
217T LEU* 4.3 24.5 - - + +
219T GLY* 4.3 14.4 - - - +
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Residues in contact with ASP 142 (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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73T HIS* 5.0 4.0 - - + -
106T PRO 5.9 0.9 - - - +
107T ILE 4.8 2.5 - - - +
108T PRO* 3.5 27.1 - - + +
109T ILE* 3.3 24.1 + - + -
110T PRO* 3.6 3.8 - - - +
140T GLY 4.1 0.6 + - - -
141T VAL* 1.3 83.4 - - - +
143T LYS* 1.3 65.1 + - - +
144T ASN* 2.9 21.0 + - - +
145T GLY 3.0 16.1 + - - +
147T HIS* 3.0 34.3 - - - -
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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