Contacts of the strand formed by residues 325 - 330 (chain C) in PDB entry 3TMP
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 325 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C VAL* 4.2 25.4 - - + -
232C GLN* 3.7 23.3 - - + -
233C VAL* 3.8 13.2 - - + -
288C MET 5.0 0.7 - - - +
292C TYR* 3.8 30.7 - - + -
294C ARG* 3.6 42.2 - - + +
295C PRO 2.8 10.9 + - - +
296C VAL* 3.2 23.2 - - + +
297C GLU 2.8 32.1 + - - +
323C GLU 3.8 0.2 + - - -
324C PRO* 1.3 69.8 - - - +
326C ARG* 1.3 55.5 + - - +
327C VAL* 4.5 6.1 - - + -
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Residues in contact with ARG 326 (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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213C PHE* 3.6 34.5 - - - -
232C GLN* 3.1 17.6 + - - +
297C GLU* 3.0 33.1 + - - +
299C TYR* 3.7 6.2 + - + -
323C GLU* 3.2 32.7 + - - +
324C PRO* 3.6 30.4 + - + +
325C ILE* 1.3 74.6 - - - +
327C VAL* 1.3 66.6 + - - +
338C VAL* 3.0 47.1 + - + +
340C ASN* 3.7 24.4 - - - +
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C LEU* 4.8 3.6 - - + -
228C ALA* 3.8 26.0 - - + +
229C VAL* 4.6 9.9 - - + -
285C MET* 4.1 8.1 - - + -
296C VAL* 4.6 4.3 - - + -
297C GLU 2.8 15.8 + - - +
298C VAL* 3.4 13.1 - - + -
299C TYR* 2.8 27.2 + - - -
325C ILE* 4.5 16.6 - - + -
326C ARG* 1.3 80.8 - - - +
328C SER* 1.3 59.4 + - - +
335C TYR* 3.8 28.0 - - + -
336C ASN 3.3 9.4 - - - +
338C VAL* 3.7 4.9 - - - -
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Residues in contact with SER 328 (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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203C PHE* 4.3 7.9 - - - -
215C ILE* 3.9 9.9 - - - +
299C TYR* 3.2 9.9 - - - -
327C VAL* 1.3 75.6 - - - +
329C TYR* 1.3 60.6 + - - +
330C HIS* 2.7 30.8 + - - -
334C HIS 3.5 0.7 - - - +
335C TYR* 3.2 10.5 - - - -
336C ASN* 2.9 42.0 + - - +
338C VAL* 3.5 18.2 - - - +
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Residues in contact with TYR 329 (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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180C GLU* 5.0 0.3 + - - -
203C PHE* 5.7 1.2 - - - -
298C VAL* 3.9 8.7 - - + -
299C TYR 2.9 14.9 + - - +
300C GLN* 3.6 44.1 + - + +
301C TYR 4.9 1.2 + - - -
328C SER* 1.3 73.4 - - - +
330C HIS* 1.3 62.7 + - - +
331C ARG 4.2 0.7 + - - -
332C ASN* 3.2 42.8 + - - -
333C ILE 3.7 2.7 - - - -
334C HIS 3.4 14.8 - - - -
335C TYR* 3.5 34.1 - + + -
40D GLN* 5.7 1.6 - - - -
72D ARG 4.2 4.6 + - - -
73D LEU* 3.2 38.6 - - + -
74D ARG 2.8 28.7 + - - -
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Residues in contact with HIS 330 (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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200C GLU* 2.9 37.2 + - - +
203C PHE* 4.4 14.9 - + - -
204C GLU* 5.9 2.7 - - + -
215C ILE* 4.1 11.6 - - + +
328C SER* 2.7 41.6 + - - -
329C TYR* 1.3 73.3 + - - +
331C ARG* 1.3 83.0 + - - +
332C ASN 2.9 6.5 + - - -
333C ILE* 3.0 11.4 + - - +
334C HIS* 2.8 27.0 + + + +
336C ASN* 3.3 30.0 + - - -
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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